Bay-annulated indigo (BAI) as an excellent electron accepting building block for high performance organic semiconductors

DOEpatents

Liu, Yi; He, Bo; Pun, Andrew

2015-11-24

A novel electron acceptor based on bay-annulated indigo (BAI) was synthesized and used for the preparation of a series of high performance donor-acceptor small molecules and polymers. The resulting materials possess low-lying LUMO energy level and small HOMO-LUMO gaps, while their films exhibited high crystallinity upon thermal treatment, commensurate with high field effect mobilities and ambipolar transfer characteristics.

Bay-annulated indigo (BAI) as an excellent electron accepting building block for high performance organic semiconductors

DOEpatents

Liu, Yi; He, Bo; Pun, Andrew

2016-04-19

A novel electron acceptor based on bay-annulated indigo (BAI) was synthesized and used for the preparation of a series of high performance donor-acceptor small molecules and polymers. The resulting materials possess low-lying LUMO energy level and small HOMO-LUMO gaps, while their films exhibited high crystallinity upon thermal treatment, commensurate with high field effect mobilities and ambipolar transfer characteristics.

Machineries regulating the activity of the small GTPase Arf6 in cancer cells are potential targets for developing innovative anti-cancer drugs.

PubMed

Yamauchi, Yohei; Miura, Yuki; Kanaho, Yasunori

2017-01-01

The Small GTPase ADP-ribosylation factor 6 (Arf6) functions as the molecular switch in cellular signaling pathways by cycling between GDP-bound inactive and GTP-bound active form, which is precisely regulated by two regulators, guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Numerous studies have shown that these machineries play critical roles in tumor angiogenesis/growth and cancer cell invasion/metastasis through regulating the cycling of Arf6. Here, we summarize accumulating knowledge for involvement of Arf6 GEFs/GAPs and small molecule inhibitors of Arf6 signaling/cycling in cancer progression, and discuss possible strategies for developing innovative anti-cancer drugs targeting Arf6 signaling/cycling. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Sleep-inducing Lipid Oleamide Deconvolutes Gap Junction Communication and Calcium Wave Transmission in Glial Cells

PubMed Central

Guan, Xiaojun; Cravatt, Benjamin F.; Ehring, George R.; Hall, James E.; Boger, Dale L.; Lerner, Richard A.; Gilula, Norton B.

1997-01-01

Oleamide is a sleep-inducing lipid originally isolated from the cerebrospinal fluid of sleep-deprived cats. Oleamide was found to potently and selectively inactivate gap junction–mediated communication between rat glial cells. In contrast, oleamide had no effect on mechanically stimulated calcium wave transmission in this same cell type. Other chemical compounds traditionally used as inhibitors of gap junctional communication, like heptanol and 18β-glycyrrhetinic acid, blocked not only gap junctional communication but also intercellular calcium signaling. Given the central role for intercellular small molecule and electrical signaling in central nervous system function, oleamide- induced inactivation of glial cell gap junction channels may serve to regulate communication between brain cells, and in doing so, may influence higher order neuronal events like sleep induction. PMID:9412472

Self-assembled nanogaps for molecular electronics.

PubMed

Tang, Qingxin; Tong, Yanhong; Jain, Titoo; Hassenkam, Tue; Wan, Qing; Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-06-17

A nanogap for molecular devices was realized using solution-based self-assembly. Gold nanorods were assembled to gold nanoparticle-coated conducting SnO2:Sb nanowires via thiol end-capped oligo(phenylenevinylene)s (OPVs). The molecular gap was easily created by the rigid molecule itself during self-assembly and the gap length was determined by the molecule length. The gold nanorods and gold nanoparticles, respectively covalently bonded at the two ends of the molecule, had very small dimensions, e.g. a width of approximately 20 nm, and hence were expected to minimize the screening effect. The ultra-long conducting SnO2:Sb nanowires provided the bridge to connect one of the electrodes of the molecular device (gold nanoparticle) to the external circuit. The tip of the atomic force microscope (AFM) was contacted onto the other electrode (gold nanorod) for the electrical measurement of the OPV device. The conductance measurement confirmed that the self-assembly of the molecules and the subsequent self-assembly of the gold nanorods was a feasible method for the fabrication of the nanogap of the molecular devices.

Adsorbing H₂S onto a single graphene sheet: A possible gas sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reshak, A. H., E-mail: maalidph@yahoo.co.uk; Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis; Auluck, S.

2014-09-14

The electronic structure of pristine graphene sheet and the resulting structure of adsorbing a single molecule of H₂S on pristine graphene in three different sites (bridge, top, and hollow) are studied using the full potential linearized augmented plane wave method. Our calculations show that the adsorption of H₂S molecule on the bridge site opens up a small direct energy gap of about 0.1 eV at symmetry point M, while adsorption of H₂S on top site opens a gap of 0.3 eV around the symmetry point K. We find that adsorbed H₂S onto the hollow site of pristine graphene sheet causesmore » to push the conduction band minimum and the valence band maximum towards Fermi level resulting in a metallic behavior. Comparing the angular momentum decomposition of the atoms projected electronic density of states of pristine graphene sheet with that of H₂S–graphene for three different cases, we find a significant influence of the location of the H₂S molecule on the electronic properties especially the strong hybridization between H₂S molecule and graphene sheet.« less

Synthesis of a low-band-gap small molecule based on acenaphthoquinoxaline for efficient bulk heterojunction solar cells.

PubMed

Mikroyannidis, J A; Kabanakis, A N; Kumar, Anil; Sharma, S S; Vijay, Y K; Sharma, G D

2010-08-03

A novel small molecule (SM) with a low-band-gap based on acenaphthoquinoxaline was synthesized and characterized. It was soluble in polar solvents such as N,N-dimethylformamide and dimethylacetamide. SM showed broad absorption curves in both solution and thin films with a long-wavelength maximum at 642 nm. The thin film absorption onset was located at 783 nm, which corresponds to an optical band gap of 1.59 eV. SM was blended with PCBM to study the donor-acceptor interactions in the blended film morphology and the photovoltaic response of the bulk heterojunction (BHJ) devices. The cyclic voltammetry measurements of the materials revealed that the HOMO and LUMO levels of SM are well aligned with those of PCBM, allowing efficient photoinduced charge transfer and suitable open circuit voltage, leading to overall power conversion efficiencies (PCEs) of approximately 2.21 and 3.23% for devices with the as-cast and thermally annealed blended layer, respectively. The increase in the PCE with the thermally annealed blend is mainly attributed to the improvement in incident photon to current efficiency (IPCE) and short circuit photocurrent (J(sc)). Thermal annealing leads to an increase in both the crystallinity of the blend and hole mobility, which improves the PCE.

Modeling Plasma Formation in a Micro-gap at Microwave Frequency

NASA Astrophysics Data System (ADS)

Bowman, Arthur; Remillard, Stephen

2013-03-01

In the presence of a strong electric field, gas molecules become ionized, forming a plasma. The study of this dielectric breakdown at microwave frequency has important applications in improving the operation of radio frequency (RF) devices, where the high electric fields present in small gaps can easily ionize gases like air. A cone and tuner resonant structure was used to induce breakdown of diatomic Nitrogen in adjustable micro-gaps ranging from 13 to 1,156 μm. The electric field for plasma formation exhibited strong pressure dependence in the larger gap sizes, as predicted by previous theoretical and experimental work. Pressure is proportional to the frequency of collision between electrons and molecules, which increases with pressure when the gap is large, but levels off in the micro-gap region. A separate model of the breakdown electric field based on the characteristic diffusion length of the plasma also fit the data poorly for these smaller gap sizes. This may be explained by a hypothesis that dielectric breakdown at and below the 100 μm gap size occurs outside the gap, an argument that is supported by the observation of very high breakdown threshold electric fields in this region. Optical emissions revealed that vibrational and rotational molecular transitions of the first positive electronic system are suppressed in micro-gaps, indicating that transitions into the molecular ground state do not occur in micro-gap plasmas. Acknowledgements: National Science Foundation under NSF-REU Grant No. PHY/DMR-1004811, the Provost's Office of Hope College, and the Hope College Division of Natural and Applied Sciences.

Structure of nascent replicative form DNA of coliphage M13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dasgupta, S.; Mitra, S.

Nascent replicative form type II (RFII) DNA of coliphage M13 synthesized in an Escherichia coli mutant deficient in the 5' ..-->.. 3' exonuclease associated with DNA polymerase I contains ribonucleotides that are retained in the covalently closed RFI DNA sealed in vitro by the joint action of T5 phage DNA polymerase and T4 phage DNA ligase. These RFI molecules are labile to alkali and RNase H, unlike the RFI produced either in vivo or from RFII with E. coli DNA polymerase I and E. coli DNA ligase. The ribonucleotides are located at one site and predominantly in one strand ofmore » the nascent RF DNA. Furthermore, these molecules contain multiple small gaps, randomly located, and one large gap in the intracistronic region.« less

Regulation of Endothelial Adherens Junctions by Tyrosine Phosphorylation

PubMed Central

Adam, Alejandro Pablo

2015-01-01

Endothelial cells form a semipermeable, regulated barrier that limits the passage of fluid, small molecules, and leukocytes between the bloodstream and the surrounding tissues. The adherens junction, a major mechanism of intercellular adhesion, is comprised of transmembrane cadherins forming homotypic interactions between adjacent cells and associated cytoplasmic catenins linking the cadherins to the cytoskeleton. Inflammatory conditions promote the disassembly of the adherens junction and a loss of intercellular adhesion, creating openings or gaps in the endothelium through which small molecules diffuse and leukocytes transmigrate. Tyrosine kinase signaling has emerged as a central regulator of the inflammatory response, partly through direct phosphorylation and dephosphorylation of the adherens junction components. This review discusses the findings that support and those that argue against a direct effect of cadherin and catenin phosphorylation in the disassembly of the adherens junction. Recent findings indicate a complex interaction between kinases, phosphatases, and the adherens junction components that allow a fine regulation of the endothelial permeability to small molecules, leukocyte migration, and barrier resealing. PMID:26556953

In silico prediction of pharmaceutical degradation pathways: a benchmarking study.

PubMed

Kleinman, Mark H; Baertschi, Steven W; Alsante, Karen M; Reid, Darren L; Mowery, Mark D; Shimanovich, Roman; Foti, Chris; Smith, William K; Reynolds, Dan W; Nefliu, Marcela; Ott, Martin A

2014-11-03

Zeneth is a new software application capable of predicting degradation products derived from small molecule active pharmaceutical ingredients. This study was aimed at understanding the current status of Zeneth's predictive capabilities and assessing gaps in predictivity. Using data from 27 small molecule drug substances from five pharmaceutical companies, the evolution of Zeneth predictions through knowledge base development since 2009 was evaluated. The experimentally observed degradation products from forced degradation, accelerated, and long-term stability studies were compared to Zeneth predictions. Steady progress in predictive performance was observed as the knowledge bases grew and were refined. Over the course of the development covered within this evaluation, the ability of Zeneth to predict experimentally observed degradants increased from 31% to 54%. In particular, gaps in predictivity were noted in the areas of epimerizations, N-dealkylation of N-alkylheteroaromatic compounds, photochemical decarboxylations, and electrocyclic reactions. The results of this study show that knowledge base development efforts have increased the ability of Zeneth to predict relevant degradation products and aid pharmaceutical research. This study has also provided valuable information to help guide further improvements to Zeneth and its knowledge base.

Self-consistent-field study of conduction through conjugated molecules

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Stafström, Sven

2001-07-01

Current-voltage (I-V) characteristics of individual molecules connected by metallic leads are studied theoretically. Using the Pariser-Parr-Pople quantum chemical method to model the molecule enables us to include electron-electron interactions in the Hartree approximation. The self-consistent-field method is used to calculate charging together with other properties for the total system under bias. Thereafter the Landauer formula is used to calculate the current from the transmission amplitudes. The most important parameter to understand charging is the position of the chemical potentials of the leads in relation to the molecular levels. At finite bias, the main part of the potential drop is located at the molecule-lead junctions. Also, the potential of the molecule is shown to partially follow the chemical potential closest to the highest occupied molecular orbital (HOMO). Therefore, the resonant tunneling steps in the I-V curves are smoothed giving a I-V resembling a ``Coulomb-gap.'' However, the charge of the molecule is not quantized since the molecule is small with quite strong interactions with the leads. The calculations predict an increase in the current at the bias corresponding to the energy gap of the molecule irrespective of the metals used in the leads. When the bias is increased further, charge is redistributed from the HOMO level to the lowest unoccupied molecular orbital of the molecule. This gives a step in the I-V curves and a corresponding change in the potential profile over the molecule. Calculations were mainly performed on polyene molecules. Molecules asymmetrically coupled to the leads model the I-V curves for molecules contacted by a scanning tunneling microscopy tip. I-V curves for pentapyrrole and another molecule that show negative differential conductance are also analyzed. The charging of these two systems depends on the shape of the molecular wave functions.

Cut-loading: a useful tool for examining the extent of gap junction tracer coupling between retinal neurons.

PubMed

Choi, Hee Joo; Ribelayga, Christophe P; Mangel, Stuart C

2012-01-12

In addition to chemical synaptic transmission, neurons that are connected by gap junctions can also communicate rapidly via electrical synaptic transmission. Increasing evidence indicates that gap junctions not only permit electrical current flow and synchronous activity between interconnected or coupled cells, but that the strength or effectiveness of electrical communication between coupled cells can be modulated to a great extent(1,2). In addition, the large internal diameter (~1.2 nm) of many gap junction channels permits not only electric current flow, but also the diffusion of intracellular signaling molecules and small metabolites between interconnected cells, so that gap junctions may also mediate metabolic and chemical communication. The strength of gap junctional communication between neurons and its modulation by neurotransmitters and other factors can be studied by simultaneously electrically recording from coupled cells and by determining the extent of diffusion of tracer molecules, which are gap junction permeable, but not membrane permeable, following iontophoretic injection into single cells. However, these procedures can be extremely difficult to perform on neurons with small somata in intact neural tissue. Numerous studies on electrical synapses and the modulation of electrical communication have been conducted in the vertebrate retina, since each of the five retinal neuron types is electrically connected by gap junctions(3,4). Increasing evidence has shown that the circadian (24-hour) clock in the retina and changes in light stimulation regulate gap junction coupling(3-8). For example, recent work has demonstrated that the retinal circadian clock decreases gap junction coupling between rod and cone photoreceptor cells during the day by increasing dopamine D2 receptor activation, and dramatically increases rod-cone coupling at night by reducing D2 receptor activation(7,8). However, not only are these studies extremely difficult to perform on neurons with small somata in intact neural retinal tissue, but it can be difficult to adequately control the illumination conditions during the electrophysiological study of single retinal neurons to avoid light-induced changes in gap junction conductance. Here, we present a straightforward method of determining the extent of gap junction tracer coupling between retinal neurons under different illumination conditions and at different times of the day and night. This cut-loading technique is a modification of scrape loading(9-12), which is based on dye loading and diffusion through open gap junction channels. Scrape loading works well in cultured cells, but not in thick slices such as intact retinas. The cut-loading technique has been used to study photoreceptor coupling in intact fish and mammalian retinas(7, 8,13), and can be used to study coupling between other retinal neurons, as described here.

Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernal, Andrés; Patiny, Luc; Castillo, Andrés M.

2015-02-21

Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruningmore » of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems.« less

Graphane versus graphene: a computational investigation of the interaction of nucleobases, aminoacids, heterocycles, small molecules (CO2, H2O, NH3, CH4, H2), metal ions and onium ions.

PubMed

Umadevi, Deivasigamani; Narahari Sastry, G

2015-11-11

Graphane has emerged as a two-dimensional hydrocarbon with interesting physical properties and potential applications. Understanding the interaction of graphane with various molecules and ions is crucial to appreciate its potential applications. We investigated the interaction of nucleobases, aminoacids, saturated and unsaturated heterocycles, small molecules, metal ions and onium ions with graphane by using density functional theory calculations. The preferred orientations of these molecules and ions on the graphane surface have been analysed. The binding energies of graphane with these molecules have been compared with the corresponding binding energies of graphene. Our results reveal that graphane forms stable complexes with all the molecules and ions yet showing lesser binding affinity when compared to graphene. As an exemption, the preferential strong binding of H2O with graphane than graphene reveals the fact that graphane is more hydrophilic than graphene. Charge transfer between graphane and the molecules and ions have been found to be an important factor in determining the binding strength of the complexes. The effect of the interaction of these molecules and ions on the HOMO-LUMO energy gap of graphane has also been investigated.

Nonadiabatic coupling reduces the activation energy in thermally activated delayed fluorescence.

PubMed

Gibson, J; Penfold, T J

2017-03-22

The temperature dependent rate of a thermally activated process is given by the Arrhenius equation. The exponential decrease in the rate with activation energy, which this imposes, strongly promotes processes with small activation barriers. This criterion is one of the most challenging during the design of thermally activated delayed fluorescence (TADF) emitters used in organic light emitting diodes. The small activation energy is usually achieved with donor-acceptor charge transfer complexes. However, this sacrifices the radiative rate and is therefore incommensurate with the high luminescence quantum yields required for applications. Herein we demonstrate that the spin-vibronic mechanism, operative for efficient TADF, overcomes this limitation. Nonadiabatic coupling between the lowest two triplet states give rise to a strong enhancement of the rate of reserve intersystem crossing via a second order mechanism and promotes population transfer between the T 1 to T 2 states. Consequently the rISC mechanism is actually operative between initial and final state exhibiting an energy gap that is smaller than between the T 1 and S 1 states. This contributes to the small activation energies for molecules exhibiting a large optical gap, identifies limitations of the present design procedures and provides a basis from which to construct TADF molecules with simultaneous high radiative and rISC rates.

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

MicroRNA Intercellular Transfer and Bioelectrical Regulation of Model Multicellular Ensembles by the Gap Junction Connectivity.

PubMed

Cervera, Javier; Meseguer, Salvador; Mafe, Salvador

2017-08-17

We have studied theoretically the microRNA (miRNA) intercellular transfer through voltage-gated gap junctions in terms of a biophysically grounded system of coupled differential equations. Instead of modeling a specific system, we use a general approach describing the interplay between the genetic mechanisms and the single-cell electric potentials. The dynamics of the multicellular ensemble are simulated under different conditions including spatially inhomogeneous transcription rates and local intercellular transfer of miRNAs. These processes result in spatiotemporal changes of miRNA, mRNA, and ion channel protein concentrations that eventually modify the bioelectrical states of small multicellular domains because of the ensemble average nature of the electrical potential. The simulations allow a qualitative understanding of the context-dependent nature of the effects observed when specific signaling molecules are transferred through gap junctions. The results suggest that an efficient miRNA intercellular transfer could permit the spatiotemporal control of small cellular domains by the conversion of single-cell genetic and bioelectric states into multicellular states regulated by the gap junction interconnectivity.

Whole-Cell-Based Assay To Evaluate Structure Permeation Relationships for Carbapenem Passage through the Pseudomonas aeruginosa Porin OprD.

PubMed

Iyer, Ramkumar; Sylvester, Mark A; Velez-Vega, Camilo; Tommasi, Ruben; Durand-Reville, Thomas F; Miller, Alita A

2017-04-14

The global emergence of antibiotic resistance, especially in Gram-negative bacteria, is an urgent threat to public health. Discovery of novel classes of antibiotics with activity against these pathogens has been impeded by a fundamental lack of understanding of the molecular drivers underlying small molecule uptake. Although it is well-known that outer membrane porins represent the main route of entry for small, hydrophilic molecules across the Gram-negative cell envelope, the structure-permeation relationship for porin passage has yet to be defined. To address this knowledge gap, we developed a sensitive and specific whole-cell approach in Escherichia coli called titrable outer membrane permeability assay system (TOMAS). We used TOMAS to characterize the structure porin-permeation relationships of a set of novel carbapenem analogues through the Pseudomonas aeruginosa porin OprD. Our results show that small structural modifications, especially the number and nature of charges and their position, have dramatic effects on the ability of these molecules to permeate cells through OprD. This is the first demonstration of a defined relationship between specific molecular changes in a substrate and permeation through an isolated porin. Understanding the molecular mechanisms that impact antibiotic transit through porins should provide valuable insights to antibacterial medicinal chemistry and may ultimately allow for the rational design of porin-mediated uptake of small molecules into Gram-negative bacteria.

Design and characterization of the first peptidomimetic molecule that prevents acidification-induced closure of cardiac gap junctions

PubMed Central

Verma, Vandana; Larsen, Bjarne Due; Coombs, Wanda; Lin, Xianming; Sarrou, Eliana; Taffet, Steven M.; Delmar, Mario

2010-01-01

Background Gap junctions are potential targets for pharmacological intervention. We have previously developed a series of peptide sequences that prevent closure of Cx43 channels, bind to cardiac Cx43 and prevent acidification-induced uncoupling of cardiac gap junctions. Objective We aimed to identify and validate the minimum core active structure in peptides containing an RR-N/Q-Y motif. Based on that information, we sought to generate a peptidomimetic molecule that acts on the chemical regulation of Cx43 channels. Methods Experiments were based on a combination of biochemical, spectroscopic and electrophysiological techniques, as well as molecular modeling of active pharmacophores with Cx43 activity. Results Molecular modeling analysis indicated that the functional elements of the side chains in the motif RRXY form a triangular structure. Experimental data revealed that compounds containing such a structure bind to Cx43 and prevent Cx43 chemical gating. These results provided us with the first platform for drug design targeted to the carboxyl terminal of Cx43. Using that platform, we designed and validated a peptidomimetic compound (ZP2519; molecular weight 619 Da) that prevented octanol-induced uncoupling of Cx43 channels, and pH gating of cardiac gap junctions. Conclusion Structure-based drug design can be applied to the development of pharmacophores that act directly on Cx43. Small molecules containing these pharmacophores can serve as tools to determine the role of gap junction regulation in the control of cardiac rhythm. Future studies will determine whether these compounds can function as pharmacological agents for the treatment of a selected subset of cardiac arrhythmias. PMID:20601149

Correlations and enlarged superconducting phase of t -J⊥ chains of ultracold molecules on optical lattices

NASA Astrophysics Data System (ADS)

Manmana, Salvatore R.; Möller, Marcel; Gezzi, Riccardo; Hazzard, Kaden R. A.

2017-10-01

We compute physical properties across the phase diagram of the t -J⊥ chain with long-range dipolar interactions, which describe ultracold polar molecules on optical lattices. Our results obtained by the density-matrix renormalization group indicate that superconductivity is enhanced when the Ising component Jz of the spin-spin interaction and the charge component V are tuned to zero and even further by the long-range dipolar interactions. At low densities, a substantially larger spin gap is obtained. We provide evidence that long-range interactions lead to algebraically decaying correlation functions despite the presence of a gap. Although this has recently been observed in other long-range interacting spin and fermion models, the correlations in our case have the peculiar property of having a small and continuously varying exponent. We construct simple analytic models and arguments to understand the most salient features.

Modulation of Brain Hemichannels and Gap Junction Channels by Pro-Inflammatory Agents and Their Possible Role in Neurodegeneration

PubMed Central

Sáez, Pablo J.; Shoji, Kenji F.; Schalper, Kurt A.; Palacios–Prado, Nicolás; Velarde, Victoria; Giaume, Christian; Bennett, Michael V.L.; Sáez, Juan C.

2009-01-01

Abstract In normal brain, neurons, astrocytes, and oligodendrocytes, the most abundant and active cells express pannexins and connexins, protein subunits of two families forming membrane channels. Most available evidence indicates that in mammals endogenously expressed pannexins form only hemichannels and connexins form both gap junction channels and hemichannels. Whereas gap junction channels connect the cytoplasm of contacting cells and coordinate electric and metabolic activity, hemichannels communicate the intra- and extracellular compartments and serve as a diffusional pathway for ions and small molecules. A subthreshold stimulation by acute pathological threatening conditions (e.g., global ischemia subthreshold for cell death) enhances neuronal Cx36 and glial Cx43 hemichannel activity, favoring ATP release and generation of preconditioning. If the stimulus is sufficiently deleterious, microglia become overactivated and release bioactive molecules that increase the activity of hemichannels and reduce gap junctional communication in astroglial networks, depriving neurons of astrocytic protective functions, and further reducing neuronal viability. Continuous glial activation triggered by low levels of anomalous proteins expressed in several neurodegenerative diseases induce glial hemichannel and gap junction channel disorders similar to those of acute inflammatory responses triggered by ischemia or infectious diseases. These changes are likely to occur in diverse cell types of the CNS and contribute to neurodegeneration during inflammatory process. Antiox. Redox Signal. 11, 369–399. PMID:18816186

Controlling the Morphology of BDTT-DPP-Based Small Molecules via End-Group Functionalization for Highly Efficient Single and Tandem Organic Photovoltaic Cells.

PubMed

Kim, Ji-Hoon; Park, Jong Baek; Yang, Hoichang; Jung, In Hwan; Yoon, Sung Cheol; Kim, Dongwook; Hwang, Do-Hoon

2015-11-04

A series of narrow-band gap, π-conjugated small molecules based on diketopyrrolopyrrole (DPP) electron acceptor units coupled with alkylthienyl-substituted-benzodithiophene (BDTT) electron donors were designed and synthesized for use as donor materials in solution-processed organic photovoltaic cells. In particular, by end-group functionalization of the small molecules with fluorine derivatives, the nanoscale morphologies of the photoactive layers of the photovoltaic cells were successfully controlled. The influences of different fluorine-based end-groups on the optoelectronic and morphological properties, carrier mobilities, and the photovoltaic performances of these materials were investigated. A high power conversion efficiency (PCE) of 6.00% under simulated solar light (AM 1.5G) illumination has been achieved for organic photovoltaic cells based on a small-molecule bulk heterojunction system consisting of a trifluoromethylbenzene (CF3) end-group-containing oligomer (BDTT-(DPP)2-CF3) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor. As a result, the introduction of CF3 end-groups has been found to enhance both the short circuit current density (JSC) and fill factor (FF). A tandem photovoltaic device comprising an inverted BDTT-(DPP)2-CF3:PC71BM cell and a poly(3-hexylthiophene) (P3HT):indene-C60-bisadduct (IC60BA)-based cell as the top and bottom cell components, respectively, showed a maximum PCE of 8.30%. These results provide valuable guidelines for the rational design of conjugated small molecules for applications in high-performance organic photovoltaic cells. Furthermore, to the best of our knowledge, this is the first report on the design of fluorine-functionalized BDTT-DPP-based small molecules, which have been shown to be a viable candidate for use in inverted tandem cells.

Single-Molecule Analysis for RISC Assembly and Target Cleavage.

PubMed

Sasaki, Hiroshi M; Tadakuma, Hisashi; Tomari, Yukihide

2018-01-01

RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.

Trap density of states in small-molecule organic semiconductors: A quantitative comparison of thin-film transistors with single crystals

NASA Astrophysics Data System (ADS)

Kalb, Wolfgang L.; Haas, Simon; Krellner, Cornelius; Mathis, Thomas; Batlogg, Bertram

2010-04-01

We show that it is possible to reach one of the ultimate goals of organic electronics: producing organic field-effect transistors with trap densities as low as in the bulk of single crystals. We studied the spectral density of localized states in the band gap [trap density of states (trap DOS)] of small-molecule organic semiconductors as derived from electrical characteristics of organic field-effect transistors or from space-charge-limited current measurements. This was done by comparing data from a large number of samples including thin-film transistors (TFT’s), single crystal field-effect transistors (SC-FET’s) and bulk samples. The compilation of all data strongly suggests that structural defects associated with grain boundaries are the main cause of “fast” hole traps in TFT’s made with vacuum-evaporated pentacene. For high-performance transistors made with small-molecule semiconductors such as rubrene it is essential to reduce the dipolar disorder caused by water adsorbed on the gate dielectric surface. In samples with very low trap densities, we sometimes observe a steep increase in the trap DOS very close (<0.15eV) to the mobility edge with a characteristic slope of 10-20 meV. It is discussed to what degree band broadening due to the thermal fluctuation of the intermolecular transfer integral is reflected in this steep increase in the trap DOS. Moreover, we show that the trap DOS in TFT’s with small-molecule semiconductors is very similar to the trap DOS in hydrogenated amorphous silicon even though polycrystalline films of small-molecules with van der Waals-type interaction on the one hand are compared with covalently bound amorphous silicon on the other hand.

Intercellular nanotubes: insights from imaging studies and beyond

PubMed Central

Hurtig, Johan; Chiu, Daniel T.; Önfelt, Björn

2017-01-01

Cell-cell communication is critical to the development, maintenance, and function of multicellular organisms. Classical mechanisms for intercellular communication include secretion of molecules into the extracellular space and transport of small molecules through gap junctions. Recent reports suggest that cells also can communicate over long distances via a network of transient intercellular nanotubes. Such nanotubes have been shown to mediate intercellular transfer of organelles as well as membrane components and cytoplasmic molecules. Moreover, intercellular nanotubes have been observed in vivo and have been shown to enhance the transmission of pathogens such as human immunodeficiency virus (HIV)-1 and prions in vitro. These studies indicate that intercellular nanotubes may play a role both in normal physiology and in disease. PMID:20166114

Benchmarking DFT and semi-empirical methods for a reliable and cost-efficient computational screening of benzofulvene derivatives as donor materials for small-molecule organic solar cells.

PubMed

Tortorella, Sara; Talamo, Maurizio Mastropasqua; Cardone, Antonio; Pastore, Mariachiara; De Angelis, Filippo

2016-02-24

A systematic computational investigation on the optical properties of a group of novel benzofulvene derivatives (Martinelli 2014 Org. Lett. 16 3424-7), proposed as possible donor materials in small molecule organic photovoltaic (smOPV) devices, is presented. A benchmark evaluation against experimental results on the accuracy of different exchange and correlation functionals and semi-empirical methods in predicting both reliable ground state equilibrium geometries and electronic absorption spectra is carried out. The benchmark of the geometry optimization level indicated that the best agreement with x-ray data is achieved by using the B3LYP functional. Concerning the optical gap prediction, we found that, among the employed functionals, MPW1K provides the most accurate excitation energies over the entire set of benzofulvenes. Similarly reliable results were also obtained for range-separated hybrid functionals (CAM-B3LYP and wB97XD) and for global hybrid methods incorporating a large amount of non-local exchange (M06-2X and M06-HF). Density functional theory (DFT) hybrids with a moderate (about 20-30%) extent of Hartree-Fock exchange (HFexc) (PBE0, B3LYP and M06) were also found to deliver HOMO-LUMO energy gaps which compare well with the experimental absorption maxima, thus representing a valuable alternative for a prompt and predictive estimation of the optical gap. The possibility of using completely semi-empirical approaches (AM1/ZINDO) is also discussed.

Quantification of gap junction selectivity.

PubMed

Ek-Vitorín, Jose F; Burt, Janis M

2005-12-01

Gap junctions, which are essential for functional coordination and homeostasis within tissues, permit the direct intercellular exchange of small molecules. The abundance and diversity of this exchange depends on the number and selectivity of the comprising channels and on the transjunctional gradient for and chemical character of the permeant molecules. Limited knowledge of functionally significant permeants and poor detectability of those few that are known have made it difficult to define channel selectivity. Presented herein is a multifaceted approach to the quantification of gap junction selectivity that includes determination of the rate constant for intercellular diffusion of a fluorescent probe (k2-DYE) and junctional conductance (gj) for each junction studied, such that the selective permeability (k2-DYE/gj) for dyes with differing chemical characteristics or junctions with differing connexin (Cx) compositions (or treatment conditions) can be compared. In addition, selective permeability can be correlated using single-channel conductance when this parameter is also measured. Our measurement strategy is capable of detecting 1) rate constants and selective permeabilities that differ across three orders of magnitude and 2) acute changes in that rate constant. Using this strategy, we have shown that 1) the selective permeability of Cx43 junctions to a small cationic dye varied across two orders of magnitude, consistent with the hypothesis that the various channel configurations adopted by Cx43 display different selective permeabilities; and 2) the selective permeability of Cx37 vs. Cx43 junctions was consistently and significantly lower.

The gap junction channel protein connexin 43 is covalently modified and regulated by SUMOylation.

PubMed

Kjenseth, Ane; Fykerud, Tone A; Sirnes, Solveig; Bruun, Jarle; Yohannes, Zeremariam; Kolberg, Matthias; Omori, Yasufumi; Rivedal, Edgar; Leithe, Edward

2012-05-04

SUMOylation is a posttranslational modification in which a member of the small ubiquitin-like modifier (SUMO) family of proteins is conjugated to lysine residues in specific target proteins. Most known SUMOylation target proteins are located in the nucleus, but there is increasing evidence that SUMO may also be a key determinant of many extranuclear processes. Gap junctions consist of arrays of intercellular channels that provide direct transfer of ions and small molecules between adjacent cells. Gap junction channels are formed by integral membrane proteins called connexins, of which the best-studied isoform is connexin 43 (Cx43). Here we show that Cx43 is posttranslationally modified by SUMOylation. The data suggest that the SUMO system regulates the Cx43 protein level and the level of functional Cx43 gap junctions at the plasma membrane. Cx43 was found to be modified by SUMO-1, -2, and -3. Evidence is provided that the membrane-proximal lysines at positions 144 and 237, located in the Cx43 intracellular loop and C-terminal tail, respectively, act as SUMO conjugation sites. Mutations of lysine 144 or lysine 237 resulted in reduced Cx43 SUMOylation and reduced Cx43 protein and gap junction levels. Altogether, these data identify Cx43 as a SUMOylation target protein and represent the first evidence that gap junctions are regulated by the SUMO system.

DFT study of adsorption behavior of NO, CO, NO2, and NH3 molecules on graphene-like BC3: A search for highly sensitive molecular sensor

NASA Astrophysics Data System (ADS)

Mehdi Aghaei, Sadegh; Monshi, M. M.; Torres, I.; Zeidi, S. M. J.; Calizo, I.

2018-01-01

The adsorption behaviors of toxic gas molecules (NO, CO, NO2, and NH3) on the graphene-like boron carbide (BC3) are investigated using first-principle density functional theory. The graphene-like BC3 monolayer is a semiconductor with a band gap of 0.733 eV. It is discovered that all the above gas molecules are chemisorbed on the BC3 sheet while they retain their molecular forms. It is also revealed that the NO2 gas molecule could be dissociated into NO and O species through the adsorption process. The amounts of charge transfer upon adsorption of CO and NH3 gas molecules on the BC3 are found to be small. The band gap changes in BC3 as a result of interactions with CO and NH3 are only 4.63% and 16.7%, indicating that the BC3-based sensor has a low and moderate sensitivity to CO and NH3, respectively. Contrariwise, upon adsorption of NO or NO2 on the BC3, significant charges are transferred from the molecules to the BC3 sheet, causing a semiconductor-metal and semiconductor-p type semiconductor transition. Our study suggests that the BC3-based sensor has a high potential for NO and NO2 detection due to the significant conductance changes, moderate adsorption energy, and short recovery time. More excitingly, the BC3 is a likely catalyst for dissociation of the NO2 gas molecule.

Physical chemistry of Nanogap-Enhanced Raman Scattering (NERS)

NASA Astrophysics Data System (ADS)

Suh, Yung Doug; Kim, Hyun Woo

2017-08-01

Plasmonically coupled electromagnetic field localization has generated a variety of new concepts and applications, and this has been one of the hottest topics in nanoscience, materials science, chemistry, physics and engineering and increasingly more important over the last decade. In particular, plasmonically coupled nanostructures with ultra-small gap ( 1-nm or smaller) gap have been of special interest due to their ultra-strong optical properties that can be useful for a variety of signal enhancements such surface-enhanced Raman scattering (SERS) and nanoantenna. These promising nanostructures with extraordinarily strong optical signal, however, have rendered a limited success in widespread use and commercialization largely due to the lack of designing principles, high-yield synthetic strategies with nm-level structural controllability and reproducibility and lack of systematic single-molecule and single-particle level studies. All these are extremely important challenges because even small changes ( 1 nm) of the coupled nanogap structures can significant affect plasmon mode and signal intensity and therefore structural and signal reproducibility and controllability can be in question. The plasmonic nanogap-enhanced Raman scattering (NERS) is defined as the plasmonic nanogap-based Raman signal enhancement within plasmonic nanogap particles with 1 nm gap and a Raman dye positioned inside the gap.

Targeting Programmed Cell Death Using Small-Molecule Compounds to Improve Potential Cancer Therapy.

PubMed

Ke, Bowen; Tian, Mao; Li, Jingjing; Liu, Bo; He, Gu

2016-11-01

Evasion of cell death is one of the hallmarks of cancer cells, beginning with long-established apoptosis and extending to other new forms of cell death. An elaboration of cell death pathways thus will contribute to a better understanding of cancer pathogenesis and therapeutics. With the recent substantial biochemical and genetic explorations of cell death subroutines, their classification has switched from primarily morphological to more molecular definitions. According to their measurable biochemical features and intricate mechanisms, cell death subroutines can be divided into apoptosis, autophagic cell death, mitotic catastrophe, necroptosis, parthanatos, ferroptosis, pyroptosis, pyronecrosis, anoikis, cornification, entosis, and NETosis. Supportive evidence has gradually revealed the prime molecular mechanisms of each subroutine and thus providing series of possible targets in cancer therapy, while the intricate relationships between different cell death subroutines still remain to be clarified. Over the past decades, cancer drug discovery has significantly benefited from the use of small-molecule compounds to target classical modalities of cell death such as apoptosis, while newly identified cell death subroutines has also emerging their potential for cancer drug discovery in recent years. In this review, we comprehensively focus on summarizing 12 cell death subroutines and discussing their corresponding small-molecule compounds in potential cancer therapy. Together, these inspiring findings may provide more evidence to fill in the gaps between cell death subroutines and small-molecule compounds to better develop novel cancer therapeutic strategies. © 2016 Wiley Periodicals, Inc.

Phenothiazine-based small-molecule organic solar cells with power conversion efficiency over 7% and open circuit voltage of about 1.0 V using solvent vapor annealing.

PubMed

Rout, Yogajivan; Misra, Rajneesh; Singhal, Rahul; Biswas, Subhayan; Sharma, Ganesh D

2018-02-28

We have used two unsymmetrical small molecules, named phenothiazine 1 and 2 with a D-A-D-π-D configuration, where phenothiazine is used as a central unit, triphenylamine is used as a terminal unit and TCBD and cyclohexa-2,5-diene-1,4-diylidene-expanded TCBD are used as an acceptor between the phenothiazine and triphenylamine units, as a small molecule donor along with PC 71 BM as an acceptor for solution processed bulk heterojunction solar cells. The variation of acceptors in the phenothiazine derivatives makes an exciting change in the photophysical and electrochemical properties, hole mobility and therefore photovoltaic performance. The optimized device based on phenothiazine 2 exhibited a high power conversion efficiency of 7.35% (J sc = 11.98 mA cm -2 , V oc = 0.99 V and FF = 0.62), while the device based on phenothiazine 1 showed a low PCE of 4.81% (J sc = 8.73 mA cm -2 , V oc = 0.95 V and FF = 0.58) after solvent vapour annealing (SVA) treatment. The higher value of power conversion efficiency of the 2 based devices irrespective of the processing conditions may be related to the broader absorption and lower band gap of 2 as compared to 1. The improvement in the SVA treated active layer may be related to the enhanced crystallinity, molecular ordering and aggregation and shorter π-π stacking distance of the small molecule donors.

Quantitative molecular orbital energies within a G0W0 approximation

NASA Astrophysics Data System (ADS)

Sharifzadeh, S.; Tamblyn, I.; Doak, P.; Darancet, P. T.; Neaton, J. B.

2012-09-01

Using many-body perturbation theory within a G 0 W 0 approximation, with a plane wave basis set and using a starting point based on density functional theory within the generalized gradient approximation, we explore routes for computing the ionization potential (IP), electron affinity (EA), and fundamental gap of three gas-phase molecules — benzene, thiophene, and (1,4) diamino-benzene — and compare with experiments. We examine the dependence of the IP and fundamental gap on the number of unoccupied states used to represent the dielectric function and the self energy, as well as the dielectric function plane-wave cutoff. We find that with an effective completion strategy for approximating the unoccupied subspace, and a well converged dielectric function kinetic energy cutoff, the computed IPs and EAs are in excellent quantitative agreement with available experiment (within 0.2 eV), indicating that a one-shot G 0 W 0 approach can be very accurate for calculating addition/removal energies of small organic molecules.

Band gap opening in α-graphyne by adsorption of organic molecule

NASA Astrophysics Data System (ADS)

Majidi, R.; Karami, A. R.

2014-09-01

The lack of a band gap limits the application of graphyne in nanoelectronic devices. We have investigated possibility of opening a band gap in α-graphyne by adsorption of tetracyanoethylene. The electronic property of α-graphyne in the presence of different numbers of tetracyanoethylene has been studied using density functional theory. It is found that charge is transferred from graphyne sheet to tetracyanoethylene molecules. In the presence of this electron acceptor molecule, a semimetal α-graphyne shows semiconducting property. The energy band gap at the Dirac point is enhanced by increasing the number of tetracyanoethylene. Our results provide a simple method to create and control the band gap in α-graphyne.

Investigation of Various Active Layers for Their Performance on Organic Solar Cells.

PubMed

Huang, Pao-Hsun; Wang, Yeong-Her; Ke, Jhong-Ciao; Huang, Chien-Jung

2016-08-09

The theoretical mechanism of open-circuit voltages (V OC ) in OSCs based on various small molecule organic materials is studied. The structure under investigation is simple planar heterojunction (PHJ) by thermal vacuum evaporation deposition. The various wide band gaps of small molecule organic materials are used to enhance the power conversion efficiency (PCE). The donor materials used in the device include: Alpha-sexithiophene (α-6T), Copper(II) phthalocyanine (CuPc), boron subnaphthalocyanine chloride (SubNc) and boron Subphthalocyanine chloride (SubPc). It is combined with fullerene or SubPc acceptor material to obtain a comprehensive understanding of the charge transport behavior. It is found that the V OC of the device is largely limited by charge transport. This was associated with the space charge effects and hole accumulation. These results are attributed to the improvement of surface roughness and work function after molybdenum trioxide (MoO₃) is inserted as an anode buffer layer.

RhoGTPase Regulators Orchestrate Distinct Stages of Synaptic Development

PubMed Central

Martin-Vilchez, Samuel; Whitmore, Leanna; Asmussen, Hannelore; Zareno, Jessica; Horwitz, Rick; Newell-Litwa, Karen

2017-01-01

Small RhoGTPases regulate changes in post-synaptic spine morphology and density that support learning and memory. They are also major targets of synaptic disorders, including Autism. Here we sought to determine whether upstream RhoGTPase regulators, including GEFs, GAPs, and GDIs, sculpt specific stages of synaptic development. The majority of examined molecules uniquely regulate either early spine precursor formation or later maturation. Specifically, an activator of actin polymerization, the Rac1 GEF β-PIX, drives spine precursor formation, whereas both FRABIN, a Cdc42 GEF, and OLIGOPHRENIN-1, a RhoA GAP, regulate spine precursor elongation. However, in later development, a novel Rac1 GAP, ARHGAP23, and RhoGDIs inactivate actomyosin dynamics to stabilize mature synapses. Our observations demonstrate that specific combinations of RhoGTPase regulatory proteins temporally balance RhoGTPase activity during post-synaptic spine development. PMID:28114311

Combining nanofluidics and plasmonics for single molecule detection

NASA Astrophysics Data System (ADS)

West, Melanie M.

Single molecule detection is limited by the small scattering cross-section of molecules which leads to weak optical signals that can be obscured by background noise. The combination of plasmonics and nanofluidics in an integrated nano-device has the potential to provide the signal enhancement necessary for the detection of single molecules. The purpose of this investigation was to optimize the fabrication of an optofluidic device that integrates a nanochannel with a plasmonic bowtie antenna. The fluidic structure of the device was fabricated using UV-nanoimprint lithography, and the gold plasmonic antennas were fabricated using a shadow evaporation and lift-off process. The effect of electron beam lithography doses on the resolution of antenna-nanochannel configurations was studied to minimize antenna gap size while maintaining the integrity of the imprinted features. The smallest antenna gap size that was achieved was 46 nm. The antennas were characterized using dark field spectroscopy to find the resonance shift, which indicated the appropriate range for optical signal enhancement. The dark field scattering results showed antennas with a broad and well-defined resonance shift that ranged from 650--800 nm. The Raman scattering results showed the highest enhancement factor (EF = 2) for antennas with an "inverted configuration," which involved having the triangles of the antenna facing back-to-back rather than the more conventional tip-to-tip bowtie arrangement.

Performance and Shock Sensitivity Evaluations of Reduced Sensitivity Explosives

NASA Astrophysics Data System (ADS)

Bowden, Patrick; Tappan, Bryce; Schmitt, Matthew; Lichthardt, Joseph; Hill, Larry

2017-06-01

Making high explosives that possess insensitivity on par with TATB-based plastic bonded explosives (PBXs), while outperforming them, has proven to be a difficult challenge. Many molecules that have challenged TATB have fallen short in either small-scale sensitivity (impact, friction), thermal stability, or possessing a shock sensitivity that is either too high or too low. Recently, an alternative approach to single-molecule-based PBXs has been blending and/or co-crystallizing explosive molecules to address shortcomings of individual components. With this approach in mind, formulations have been prepared containing 1,1-diamino-2,2-dinitroethene (DADNE or FOX-7) or 3,3'-diamino-4,4'-azoxyfurazan (DAAF) with 3-nitro-1,2,4-triazole-5-one (NTO). Detailed characterization of these mixtures has been described in a concurrent study. Here we focus on in depth performance metrics such as cylinder wall expansion and CJ pressure (via free surface velocity) and shock sensitivity, by small-scale gap-testing, were investigated as a function of weight percentages of the components. Results will be contrasted with known insensitive high explosives.

Deep absorbing porphyrin small molecule for high-performance organic solar cells with very low energy losses.

PubMed

Gao, Ke; Li, Lisheng; Lai, Tianqi; Xiao, Liangang; Huang, Yuan; Huang, Fei; Peng, Junbiao; Cao, Yong; Liu, Feng; Russell, Thomas P; Janssen, René A J; Peng, Xiaobin

2015-06-17

We designed and synthesized the DPPEZnP-TEH molecule, with a porphyrin ring linked to two diketopyrrolopyrrole units by ethynylene bridges. The resulting material exhibits a very low energy band gap of 1.37 eV and a broad light absorption to 907 nm. An open-circuit voltage of 0.78 V was obtained in bulk heterojunction (BHJ) organic solar cells, showing a low energy loss of only 0.59 eV, which is the first report that small molecule solar cells show energy losses <0.6 eV. The optimized solar cells show remarkable external quantum efficiency, short circuit current, and power conversion efficiency up to 65%, 16.76 mA/cm(2), and 8.08%, respectively, which are the best values for BHJ solar cells with very low energy losses. Additionally, the morphology of DPPEZnP-TEH neat and blend films with PC61BM was studied thoroughly by grazing incidence X-ray diffraction, resonant soft X-ray scattering, and transmission electron microscopy under different fabrication conditions.

Quasiparticle band gap of organic-inorganic hybrid perovskites: Crystal structure, spin-orbit coupling, and self-energy effects

NASA Astrophysics Data System (ADS)

Gao, Weiwei; Gao, Xiang; Abtew, Tesfaye A.; Sun, Yi-Yang; Zhang, Shengbai; Zhang, Peihong

2016-02-01

The quasiparticle band gap is one of the most important materials properties for photovoltaic applications. Often the band gap of a photovoltaic material is determined (and can be controlled) by various factors, complicating predictive materials optimization. An in-depth understanding of how these factors affect the size of the gap will provide valuable guidance for new materials discovery. Here we report a comprehensive investigation on the band gap formation mechanism in organic-inorganic hybrid perovskites by decoupling various contributing factors which ultimately determine their electronic structure and quasiparticle band gap. Major factors, namely, quasiparticle self-energy, spin-orbit coupling, and structural distortions due to the presence of organic molecules, and their influences on the quasiparticle band structure of organic-inorganic hybrid perovskites are illustrated. We find that although methylammonium cations do not contribute directly to the electronic states near band edges, they play an important role in defining the band gap by introducing structural distortions and controlling the overall lattice constants. The spin-orbit coupling effects drastically reduce the electron and hole effective masses in these systems, which is beneficial for high carrier mobilities and small exciton binding energies.

Spatio-temporal regulation of connexin43 phosphorylation and gap junction dynamics.

PubMed

Solan, Joell L; Lampe, Paul D

2018-01-01

Gap junctions are specialized membrane domains containing tens to thousands of intercellular channels. These channels permit exchange of small molecules (<1000Da) including ions, amino acids, nucleotides, metabolites and secondary messengers (e.g., calcium, glucose, cAMP, cGMP, IP 3 ) between cells. The common reductionist view of these structures is that they are composed entirely of integral membrane proteins encoded by the 21 member connexin human gene family. However, it is clear that the normal physiological function of this structure requires interaction and regulation by a variety of proteins, especially kinases. Phosphorylation is capable of directly modulating connexin channel function but the most dramatic effects on gap junction activity occur via the organization of the gap junction structures themselves. This is a direct result of the short half-life of the primary gap junction protein, connexin, which requires them to be constantly assembled, remodeled and turned over. The biological consequences of this remodeling are well illustrated during cardiac ischemia, a process wherein gap junctions are disassembled and remodeled resulting in arrhythmia and ultimately heart failure. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve. Copyright © 2017 Elsevier B.V. All rights reserved.

Hexadecameric structure of an invertebrate gap junction channel.

PubMed

Oshima, Atsunori; Matsuzawa, Tomohiro; Murata, Kazuyoshi; Tani, Kazutoshi; Fujiyoshi, Yoshinori

2016-03-27

Innexins are invertebrate-specific gap junction proteins with four transmembrane helices. These proteins oligomerize to constitute intercellular channels that allow for the passage of small signaling molecules associated with neural and muscular electrical activity. In contrast to the large number of structural and functional studies of connexin gap junction channels, few structural studies of recombinant innexin channels are reported. Here we show the three-dimensional structure of two-dimensionally crystallized Caenorhabditis elegans innexin-6 (INX-6) gap junction channels. The N-terminal deleted INX-6 proteins are crystallized in lipid bilayers. The three-dimensional reconstruction determined by cryo-electron crystallography reveals that a single INX-6 gap junction channel comprises 16 subunits, a hexadecamer, in contrast to chordate connexin channels, which comprise 12 subunits. The channel pore diameters at the cytoplasmic entrance and extracellular gap region are larger than those of connexin26. Two bulb densities are observed in each hemichannel, one in the pore and the other at the cytoplasmic side of the hemichannel in the channel pore pathway. These findings imply a structural diversity of gap junction channels among multicellular organisms. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

From the Kohn-Sham band gap to the fundamental gap in solids. An integer electron approach.

PubMed

Baerends, E J

2017-06-21

It is often stated that the Kohn-Sham occupied-unoccupied gap in both molecules and solids is "wrong". We argue that this is not a correct statement. The KS theory does not allow to interpret the exact KS HOMO-LUMO gap as the fundamental gap (difference (I - A) of electron affinity (A) and ionization energy (I), twice the chemical hardness), from which it indeed differs, strongly in molecules and moderately in solids. The exact Kohn-Sham HOMO-LUMO gap in molecules is much below the fundamental gap and very close to the much smaller optical gap (first excitation energy), and LDA/GGA yield very similar gaps. In solids the situation is different: the excitation energy to delocalized excited states and the fundamental gap (I - A) are very similar, not so disparate as in molecules. Again the Kohn-Sham and LDA/GGA band gaps do not represent (I - A) but are significantly smaller. However, the special properties of an extended system like a solid make it very easy to calculate the fundamental gap from the ground state (neutral system) band structure calculations entirely within a density functional framework. The correction Δ from the KS gap to the fundamental gap originates from the response part v resp of the exchange-correlation potential and can be calculated very simply using an approximation to v resp . This affords a calculation of the fundamental gap at the same level of accuracy as other properties of crystals at little extra cost beyond the ground state bandstructure calculation. The method is based on integer electron systems, fractional electron systems (an ensemble of N- and (N + 1)-electron systems) and the derivative discontinuity are not invoked.

The synthesis and properties of linear A-π-D-π-A type organic small molecule containing diketopyrrolopyrrole terminal units.

PubMed

Zhang, Shanshan; Niu, Qingfen; Sun, Tao; Li, Yang; Li, Tianduo; Liu, Haixia

2017-08-05

A novel linear A-π-D-π-A-type organic small molecule Ph2(PDPP) 2 consisting diketopyrrolopyrrole (DPP) as acceptor unit, biphenylene as donor unit and acetylene unit as π-linkage has been successfully designed and synthesized. Its corresponding thermal, photophysical and electrochemical properties as well as the photoinduced charge-separation process were investigated. Ph2(PDPP) 2 exhibits high thermal stability and it can be soluble in common organic solvents such as chloroform and tetrahydrofuran. The photophysical properties show that DPP 2 Ph 2 harvests sunlight over the entire visible spectrum range in the thin-film state (300-800nm). DPP 2 Ph 2 has lower band gaps and appropriate energy levels to satisfy the requirement of solution-processable organic solar cells. The efficient photoinduced charge separation process was clearly observed between DPP 2 Ph 2 with PC 61 BM and the K sv value was found to be as high as 2.13×10 4 M -1 . Therefore, these excellent properties demonstrate that the designed A-π-D-π-A-type small molecule Ph2(PDPP) 2 is the prospective candidate as donor material for organic photovoltaic material. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-Assembled Polystyrene Beads for Templated Covalent Functionalization of Graphitic Substrates Using Diazonium Chemistry.

PubMed

Van Gorp, Hans; Walke, Peter; Bragança, Ana M; Greenwood, John; Ivasenko, Oleksandr; Hirsch, Brandon E; De Feyter, Steven

2018-04-11

A network of self-assembled polystyrene beads was employed as a lithographic mask during covalent functionalization reactions on graphitic surfaces to create nanocorrals for confined molecular self-assembly studies. The beads were initially assembled into hexagonal arrays at the air-liquid interface and then transferred to the substrate surface. Subsequent electrochemical grafting reactions involving aryl diazonium molecules created covalently bound molecular units that were localized in the void space between the nanospheres. Removal of the bead template exposed hexagonally arranged circular nanocorrals separated by regions of chemisorbed molecules. Small molecule self-assembly was then investigated inside the resultant nanocorrals using scanning tunneling microscopy to highlight localized confinement effects. Overall, this work illustrates the utility of self-assembly principles to transcend length scale gaps in the development of hierarchically patterned molecular materials.

Gap Junction Inhibition Prevents Drug-induced Liver Toxicity and Fulminant Hepatic Failure

PubMed Central

Patel, Suraj J; Milwid, Jack M; King, Kevin R; Bohr, Stefan; Iracheta, Arvin; Li, Matthew; Vitalo, Antonia; Parekkadan, Biju; Jindal, Rohit; Yarmush, Martin L

2013-01-01

Drug-induced liver injury (DILI) limits the development and utilization of numerous therapeutic compounds, and consequently presents major challenges to the pharmaceutical industry and clinical medicine1, 2. Acetaminophen (APAP) containing compounds are among the most frequently prescribed drugs, and also the most common cause of DILI3. Here we describe a pharmacological strategy that targets gap junction communication to prevent amplification of fulminant hepatic failure and APAP-induced hepatotoxicity. We report that connexin 32 (Cx32), a key hepatic gap junction protein, is an essential mediator of DILI by showing that mice deficient in Cx32 are protected against liver damage, acute inflammation, and death. We identified a small molecule inhibitor of Cx32 as a novel hepatoprotectant that achieves the same result in wildtype mice when coadministered with known hepatotoxic drugs. These findings demonstrate that gap junction inhibition is an effective therapy for limiting DILI, and suggest a novel pharmaceutical strategy to improve drug safety. PMID:22252509

Spontaneous nano-gap formation in Ag film using NaCl sacrificial layer for Raman enhancement

NASA Astrophysics Data System (ADS)

Min, Kyungchan; Jeon, Wook Jin; Kim, Youngho; Choi, Jae-Young; Yu, Hak Ki

2018-03-01

We report the method of fabrication of nano-gaps (known as hot spots) in Ag thin film using a sodium chloride (NaCl) sacrificial layer for Raman enhancement. The Ag thin film (20-50 nm) on the NaCl sacrificial layer undergoes an interfacial reaction due to the AgCl formed at the interface during water molecule intercalation. The intercalated water molecules can dissolve the NaCl molecules at interfaces and form the ionic state of Na+ and Cl-, promoting the AgCl formation. The Ag atoms can migrate by the driving force of this interfacial reaction, resulting in the formation of nano-size gaps in the film. The surface-enhanced Raman scattering activity of Ag films with nano-size gaps has been investigated using Raman reporter molecules, Rhodamine 6G (R6G).

A systematic benchmark of the ab initio Bethe-Salpeter equation approach for low-lying optical excitations of small organic molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruneval, Fabien; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Department of Physics, University of California, Berkeley, California 94720

2015-06-28

The predictive power of the ab initio Bethe-Salpeter equation (BSE) approach, rigorously based on many-body Green’s function theory but incorporating information from density functional theory, has already been demonstrated for the optical gaps and spectra of solid-state systems. Interest in photoactive hybrid organic/inorganic systems has recently increased and so has the use of the BSE for computing neutral excitations of organic molecules. However, no systematic benchmarks of the BSE for neutral electronic excitations of organic molecules exist. Here, we study the performance of the BSE for the 28 small molecules in Thiel’s widely used time-dependent density functional theory benchmark setmore » [Schreiber et al., J. Chem. Phys. 128, 134110 (2008)]. We observe that the BSE produces results that depend critically on the mean-field starting point employed in the perturbative approach. We find that this starting point dependence is mainly introduced through the quasiparticle energies obtained at the intermediate GW step and that with a judicious choice of starting mean-field, singlet excitation energies obtained from BSE are in excellent quantitative agreement with higher-level wavefunction methods. The quality of the triplet excitations is slightly less satisfactory.« less

Mildly reduced graphene oxide-Ag nanoparticle hybrid films for surface-enhanced Raman scattering

PubMed Central

2012-01-01

Large-area mildly reduced graphene oxide (MR-GO) monolayer films were self-assembled on SiO2/Si surfaces via an amidation reaction strategy. With the MR-GO as templates, MR-GO-Ag nanoparticle (MR-GO-Ag NP) hybrid films were synthesized by immersing the MR-GO monolayer into a silver salt solution with sodium citrate as a reducing agent under UV illumination. SEM image indicated that Ag NPs with small interparticle gap are uniformly distributed on the MR-GO monolayer. Raman spectra demonstrated that the MR-GO monolayer beneath the Ag NPs can effectively quench the fluorescence signal emitted from the Ag films and dye molecules under laser excitation, resulting in a chemical enhancement (CM). The Ag NPs with narrow gap provided numerous hot spots, which are closely related with electromagnetic mechanism (EM), and were believed to remarkably enhance the Raman signal of the molecules. Due to the co-contribution of the CM and EM effects as well as the coordination mechanism between the MR-GO and Ag NPs, the MR-GO-Ag NP hybrid films showed more excellent Raman signal enhancement performance than that of either Ag films or MR-GO monolayer alone. This will further enrich the application of surface-enhanced Raman scattering in molecule detection. PMID:22471923

CH3Br adsorption on MgO/Mo ultrathin films: A DFT study

NASA Astrophysics Data System (ADS)

Cipriano, Luis A.; Tosoni, Sergio; Pacchioni, Gianfranco

2018-06-01

The adsorption of methyl bromide on MgO ultrathin films supported on Mo(100) was studied by means of density functional theory calculations, in comparison to the MgO(100) and Mo(100) surfaces. The adsorption energy and geometry were shown to depend on the thickness of the supported oxide film. MgO films as thick as 2ML (or more) display adsorptive properties similar to MgO(100), i.e. the adsorption of CH3Br is mostly due to dispersion and the molecule lies in a tilted geometry almost parallel to the surface. The CH3Br HOMO-LUMO gap is almost unaltered with respect to the gas phase. On metallic Mo(100) surfaces the bonding is completely different with the CH3Br molecule strongly bound and the C-Br bond axis almost vertical with respect to the metal surface. The MgO monolayer supported on Mo exhibits somehow intermediate properties: the tilt angle is larger and the bonding is stronger than on MgO(100), due to the effect of the supporting metal. In this case, a small reduction of the HOMO-LUMO gap of the adsorbed molecule is reported. The results help to rationalize the observed behavior in photodissociation of CH3Br supported on different substrates.

Gap junctions in cells of the immune system: structure, regulation and possible functional roles.

PubMed

Sáez, J C; Brañes, M C; Corvalán, L A; Eugenín, E A; González, H; Martínez, A D; Palisson, F

2000-04-01

Gap junction channels are sites of cytoplasmic communication between contacting cells. In vertebrates, they consist of protein subunits denoted connexins (Cxs) which are encoded by a gene family. According to their Cx composition, gap junction channels show different gating and permeability properties that define which ions and small molecules permeate them. Differences in Cx primary sequences suggest that channels composed of different Cxs are regulated differentially by intracellular pathways under specific physiological conditions. Functional roles of gap junction channels could be defined by the relative importance of permeant substances, resulting in coordination of electrical and/or metabolic cellular responses. Cells of the native and specific immune systems establish transient homo- and heterocellular contacts at various steps of the immune response. Morphological and functional studies reported during the last three decades have revealed that many intercellular contacts between cells in the immune response present gap junctions or "gap junction-like" structures. Partial characterization of the molecular composition of some of these plasma membrane structures and regulatory mechanisms that control them have been published recently. Studies designed to elucidate their physiological roles suggest that they might permit coordination of cellular events which favor the effective and timely response of the immune system.

Structural basis for the selective permeability of channels made of communicating junction proteins

PubMed Central

Ek-Vitorin, Jose F.; Burt, Janis M.

2012-01-01

The open state(s) of gap junction channels is evident from their permeation by small ions in response to an applied intercellular (transjunctional/transchannel) voltage gradient. That an open channel allows variable amounts of current to transit from cell-to-cell in the face of a constant intercellular voltage difference indicates channel open/closing can be complete or partial. The physiological significance of such open state options is, arguably, the main concern of junctional regulation. Because gap junctions are permeable to many substances, it is sensible to inquire whether and how each open state influences the intercellular diffusion of molecules as valuable as, but less readily detected than current-carrying ions. Presumably, structural changes perceived as shifts in channel conductivity would significantly alter the transjunctional diffusion of molecules whose limiting diameter approximates the pore’s limiting diameter. Moreover, changes in junctional permeability to some molecules might occur without evident changes in conductivity, either at macroscopic or single channel level. Open gap junction channels allow the exchange of cytoplasmic permeants between contacting cells by simple diffusion. The identity of such permeants, and the functional circumstances and consequences of their junctional exchange presently constitute the most urgent (and demanding) themes of the field. Here, we consider the necessity for regulating this exchange, the possible mechanism(s) and structural elements likely involved in such regulation, and how regulatory phenomena could be perceived as changes in chemical vs. electrical coupling; an overall reflection on our collective knowledge of junctional communication is then applied to suggest new avenues of research. PMID:22342665

Varespladib (LY315920) Appears to Be a Potent, Broad-Spectrum, Inhibitor of Snake Venom Phospholipase A2 and a Possible Pre-Referral Treatment for Envenomation

PubMed Central

Lewin, Matthew; Samuel, Stephen; Merkel, Janie; Bickler, Philip

2016-01-01

Snakebite remains a neglected medical problem of the developing world with up to 125,000 deaths each year despite more than a century of calls to improve snakebite prevention and care. An estimated 75% of fatalities from snakebite occur outside the hospital setting. Because phospholipase A2 (PLA2) activity is an important component of venom toxicity, we sought candidate PLA2 inhibitors by directly testing drugs. Surprisingly, varespladib and its orally bioavailable prodrug, methyl-varespladib showed high-level secretory PLA2 (sPLA2) inhibition at nanomolar and picomolar concentrations against 28 medically important snake venoms from six continents. In vivo proof-of-concept studies with varespladib had striking survival benefit against lethal doses of Micrurus fulvius and Vipera berus venom, and suppressed venom-induced sPLA2 activity in rats challenged with 100% lethal doses of M. fulvius venom. Rapid development and deployment of a broad-spectrum PLA2 inhibitor alone or in combination with other small molecule inhibitors of snake toxins (e.g., metalloproteases) could fill the critical therapeutic gap spanning pre-referral and hospital setting. Lower barriers for clinical testing of safety tested, repurposed small molecule therapeutics are a potentially economical and effective path forward to fill the pre-referral gap in the setting of snakebite. PMID:27571102

Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

PubMed Central

2017-01-01

Metal–molecule–metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution, we highlight the fundamental differences between single-molecule and ensemble junctions focusing on the fundamentals of transport through molecular clusters. In this way, we elucidate the collective behavior of parallel molecular wires, bridging the gap between single molecule and large-area monolayer electronics, where even in the latter case transport is usually dominated by finite-size islands. On the basis of first-principles charge-transport simulations, we explain why the scaling of the conductivity of a junction has to be distinctly nonlinear in the number of molecules it contains. Moreover, transport through molecular clusters is found to be highly inhomogeneous with pronounced edge effects determined by molecules in locally different electrostatic environments. These effects are most pronounced for comparably small clusters, but electrostatic considerations show that they prevail also for more extended systems. PMID:29043825

Mapping small molecule binding data to structural domains

PubMed Central

2012-01-01

Background Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. Results In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. Conclusions Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies. PMID:23282026

Oligothiophene-Indandione-Linked Narrow-Band Gap Molecules: Impact of π-Conjugated Chain Length on Photovoltaic Performance.

PubMed

Komiyama, Hideaki; To, Takahiro; Furukawa, Seiichi; Hidaka, Yu; Shin, Woong; Ichikawa, Takahiro; Arai, Ryota; Yasuda, Takuma

2018-04-04

Solution-processed organic solar cells (OSCs) based on narrow-band gap small molecules hold great promise as next-generation energy-converting devices. In this paper, we focus on a family of A-π-D-π-A-type small molecules, namely, BDT- nT-ID ( n = 1-4) oligomers, consisting of benzo[1,2- b:4,5- b']dithiophene (BDT) as the central electron-donating (D) core, 1,3-indandione (ID) as the terminal electron-accepting (A) units, and two regioregular oligo(3-hexylthiophene)s ( nT) with different numbers of thiophene rings as the π-bridging units, and elucidate their structure-property-function relationships. The effects of the length of the π-bridging nT units on the optical absorption, thermal behavior, morphology, hole mobility, and OSC performance were systematically investigated. All oligomers exhibited broad and intense visible photoabsorption in the 400-700 nm range. The photovoltaic performances of bulk heterojunction OSCs based on BDT- nT-IDs as donors and a fullerene derivative as an acceptor were studied. Among these oligomers, BDT-2T-ID, incorporating bithiophene as the π-bridging units, showed better photovoltaic performance with a maximum power conversion efficiency as high as 6.9% under AM 1.5G illumination without using solvent additives or postdeposition treatments. These favorable properties originated from the well-developed interpenetrating network morphology of BDT-2T-ID, with larger domain sizes in the photoactive layer. Even though all oligomers have the same A-D-A main backbone, structural modulation of the π-bridging nT length was found to impact their self-organization and nanostructure formation in the solid state, as well as the corresponding OSC device performance.

Emergence of complex chemistry on an organic monolayer.

PubMed

Prins, Leonard J

2015-07-21

In many origin-of-life scenarios, inorganic materials, such as FeS or mineral clays, play an important role owing to their ability to concentrate and select small organic molecules on their surface and facilitate their chemical transformations into new molecules. However, considering that life is made up of organic matter, at a certain stage during the evolution the role of the inorganic material must have been taken over by organic molecules. How this exactly happened is unclear, and, indeed, a big gap separates the rudimentary level of organization involving inorganic materials and the complex organization of cells, which are the building blocks of life. Over the past years, we have extensively studied the interaction of small molecules with monolayer-protected gold nanoparticles (Au NPs) for the purpose of developing innovative sensing and catalytic systems. During the course of these studies, we realized that the functional role of this system is very similar to that typically attributed to inorganic surfaces in the early stages of life, with the important being difference that the functional properties (molecular recognition, catalysis, signaling, adaptation) originate entirely from the organic monolayer rather than the inorganic support. This led us to the proposition that this system may serve as a model that illustrates how the important role of inorganic surfaces in dictating chemical processes in the early stages of life may have been taken over by organic matter. Here, we reframe our previously obtained results in the context of the origin-of-life question. The following functional roles of Au NPs will be discussed: the ability to concentrate small molecules and create different local populations, the ability to catalyze the chemical transformation of bound molecules, and, finally, the ability to install rudimentary signaling pathways and display primitive adaptive behavior. In particular, we will show that many of the functional properties of the system originate from two features: the presence of metal ions that are complexed in the organic monolayer and the multivalent nature of the system. Complexed metal ions play an important role in determining the affinity and selectivity of the interaction with small molecules, but serve also as regulatory elements for determining how many molecules are bound simultaneously. Importantly, neighboring metal ion complexes also create catalytic pockets in which two metal ions cooperatively catalyze the cleavage of an RNA-model compound. The multivalent nature of the system permits multiple noncovalent interactions with small molecules that enhances the affinity, but is also at the basis of simple signal transduction pathways and adaptive behavior.

Non-fluorescent nanoscopic monitoring of a single trapped nanoparticle via nonlinear point sources.

PubMed

Yoon, Seung Ju; Lee, Jungmin; Han, Sangyoon; Kim, Chang-Kyu; Ahn, Chi Won; Kim, Myung-Ki; Lee, Yong-Hee

2018-06-07

Detection of single nanoparticles or molecules has often relied on fluorescent schemes. However, fluorescence detection approaches limit the range of investigable nanoparticles or molecules. Here, we propose and demonstrate a non-fluorescent nanoscopic trapping and monitoring platform that can trap a single sub-5-nm particle and monitor it with a pair of floating nonlinear point sources. The resonant photon funnelling into an extremely small volume of ~5 × 5 × 7 nm 3 through the three-dimensionally tapered 5-nm-gap plasmonic nanoantenna enables the trapping of a 4-nm CdSe/ZnS quantum dot with low intensity of a 1560-nm continuous-wave laser, and the pumping of 1560-nm femtosecond laser pulses creates strong background-free second-harmonic point illumination sources at the two vertices of the nanoantenna. Under the stable trapping conditions, intermittent but intense nonlinear optical spikes are observed on top of the second-harmonic signal plateau, which is identified as the 3.0-Hz Kramers hopping of the quantum dot trapped in the 5-nm gap.

Formation of Enhanced Uniform Chiral Fields in Symmetric Dimer Nanostructures

PubMed Central

Tian, Xiaorui; Fang, Yurui; Sun, Mengtao

2015-01-01

Chiral fields with large optical chirality are very important in chiral molecules analysis, sensing and other measurements. Plasmonic nanostructures have been proposed to realize such super chiral fields for enhancing weak chiral signals. However, most of them cannot provide uniform chiral near-fields close to the structures, which makes these nanostructures not so efficient for applications. Plasmonic helical nanostructures and blocked squares have been proved to provide uniform chiral near-fields, but structure fabrication is a challenge. In this paper, we show that very simple plasmonic dimer structures can provide uniform chiral fields in the gaps with large enhancement of both near electric fields and chiral fields under linearly polarized light illumination with polarization off the dimer axis at dipole resonance. An analytical dipole model is utilized to explain this behavior theoretically. 30 times of volume averaged chiral field enhancement is gotten in the whole gap. Chiral fields with opposite handedness can be obtained simply by changing the polarization to the other side of the dimer axis. It is especially useful in Raman optical activity measurement and chiral sensing of small quantity of chiral molecule. PMID:26621558

Sensitive detection of surface- and size-dependent direct and indirect band gap transitions in ferritin.

PubMed

Colton, J S; Erickson, S D; Smith, T J; Watt, R K

2014-04-04

Ferritin is a protein nano-cage that encapsulates minerals inside an 8 nm cavity. Previous band gap measurements on the native mineral, ferrihydrite, have reported gaps as low as 1.0 eV and as high as 2.5-3.5 eV. To resolve this discrepancy we have used optical absorption spectroscopy, a well-established technique for measuring both direct and indirect band gaps. Our studies included controls on the protein nano-cage, ferritin with the native ferrihydrite mineral, and ferritin with reconstituted ferrihydrite cores of different sizes. We report measurements of an indirect band gap for native ferritin of 2.140 ± 0.015 eV (579.7 nm), with a direct transition appearing at 3.053 ± 0.005 eV (406.1 nm). We also see evidence of a defect-related state having a binding energy of 0.220 ± 0.010 eV . Reconstituted ferrihydrite minerals of different sizes were also studied and showed band gap energies which increased with decreasing size due to quantum confinement effects. Molecules that interact with the surface of the mineral core also demonstrated a small influence following trends in ligand field theory, altering the native mineral's band gap up to 0.035 eV.

Alcohol molecules adsorption on graphane nanosheets - A first-principles investigation

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Chandiramouli, R.

2018-05-01

The geometric structure, electronic and adsorption properties of methanol, ethanol and 1-propanol molecules on hydrogenated graphene (graphane) were investigated using first-principles calculations. The stability of graphane base material is confirmed using formation energy and phonon band structures. The adsorption of alcohol molecules on bare graphane and hydrogen vacant graphane nanosheet is found to be prominent and the selectivity of alcohol molecules can be achieved using bare or hydrogen vacant graphane nanosheet. Moreover, the interaction of alcohol molecules on bare and hydrogen vacant graphane nanosheets is studied using the adsorption energy, energy band gap variation, Bader charge transfer and average energy band gap variation. The adsorption energy ranges from -0.149 to -0.383 eV upon alcohol adsorption. The energy gap varies from 4.71 to 2.62 eV for bare graphane and from 4.02 to 3.60 eV for hydrogen vacant graphane nanosheets upon adsorption of alcohol molecules. The adsorption properties of alcohol molecules provide useful information for the possible application of graphane nanosheet as a base material for the detection of alcohol molecules.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Öner, Nazmiye, E-mail: fizikcinaz@gmail.com; Tamer, Ömer, E-mail: omertamer@sakarya.edu.tr; Avci, Davut, E-mail: davci@sakarya.edu.tr

Quantum mechanical calculations on cis-2, 6-bis (2-chlorophenyl)-3, 3-dimethylpiperidin-4-one were performed by using HSEH1PBE level of density functional theory (DFT) with 6-311++G (d, p) basis set. Geometric parameters of the title molecule in the ground state were found to be in good agreement with experimental data. The frontier molecular orbitals (HOMO and LUMO) were simulated by the same level. Small energy gap between the HOMO and LUMO is an indicator molecular charge transfer within the title molecule. The electronegativity, chemical hardness and softness were also calculated by using HOMO and LUMO energies. Dipole moment, polarizability and hyperpolarizability parameters were also calculatedmore » by using HSEH1PBE level. All calculations were carried out with the GAUSSIAN 09 package program.« less

Microgravity and Signaling Molecules in Rat Osteoblasts: Downstream of Receptor Tyrosine Kinase, G-Protein-Coupled Receptor, and Small GTP-Binding Proteins

NASA Technical Reports Server (NTRS)

Kumel, Yasuhiro; Shimokawa, Hitoyata; Morita, Sadao; Katano, Hisako; Akiyama, Hideo; Hirano, Masahiko; Ohya, Keiichi; Sams, Clarence F.; Whitson, Peggy A.

2005-01-01

Rat osteoblasts were cultured for 4 and 5 days aboard Space Shuttle and solubilized on board. The mRNA levels of the post-receptor signaling molecules were analyzed by quantitative RT-PCR. The G-protein alpha subunit G(alpha)q mRNA levels were elevated 3-fold by microgravity. G(alpha)q stimulates PLC(beta), and then PKC. PKC(delta) and PKC(theta) mRNA levels were increased 2- to 5-fold by microgravity The mRNA levels of SOS and Ras GRF were increased 4 to 5-fold by microgravity, while Ras GAP was not altered. Spaceflight-induced bone loss might be attributed to microgravity modulation of the signaling pathway in osteoblasts.

Toward High Performance Photovoltaic Cells based on Conjugated Polymers

DTIC Science & Technology

2016-12-26

AFRL-AFOSR-JP-TR-2016-0103 Toward High Performance Photovoltaic Cells based on Conjugated Polymers Kung-Hwa Wei National Chiao Tung University Final...Conjugated Polymers 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-15-1-4113 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) Kung-Hwa Wei 5d.  PROJECT...gap polymer with good packing order as the active layer for a single-junction photovoltaic device. The light absorptions for the small molecule and the

Valence-band structure of organic radical p-CF3PNN investigated by angle-resolved photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Anzai, Hiroaki; Takakura, Ryosuke; Ono, Yusuke; Ishihara, Suzuna; Sato, Hitoshi; Namatame, Hirofumi; Taniguchi, Masaki; Matsui, Toshiyuki; Noguchi, Satoru; Hosokoshi, Yuko

2018-05-01

We study the electronic structure of p-trifluoromethylphenyl nitronyl nitroxide (p-CF3PNN), which forms a one-dimensional alternating antiferromagnetic chain of molecules, using angle-resolved photoemission spectroscopy. A singly occupied molecular orbital (SOMO) is observed clearly at ∼ 2 eV in the valence-band spectra. The small band gap and the overlap between the SOMO orbitals in the NO groups are associated with the antiferromagnetic interaction between neighboring spins.

Structural basis for the selective permeability of channels made of communicating junction proteins.

PubMed

Ek-Vitorin, Jose F; Burt, Janis M

2013-01-01

The open state(s) of gap junction channels is evident from their permeation by small ions in response to an applied intercellular (transjunctional/transchannel) voltage gradient. That an open channel allows variable amounts of current to transit from cell-to-cell in the face of a constant intercellular voltage difference indicates channel open/closing can be complete or partial. The physiological significance of such open state options is, arguably, the main concern of junctional regulation. Because gap junctions are permeable to many substances, it is sensible to inquire whether and how each open state influences the intercellular diffusion of molecules as valuable as, but less readily detected than current-carrying ions. Presumably, structural changes perceived as shifts in channel conductivity would significantly alter the transjunctional diffusion of molecules whose limiting diameter approximates the pore's limiting diameter. Moreover, changes in junctional permeability to some molecules might occur without evident changes in conductivity, either at macroscopic or single channel level. Open gap junction channels allow the exchange of cytoplasmic permeants between contacting cells by simple diffusion. The identity of such permeants, and the functional circumstances and consequences of their junctional exchange presently constitute the most urgent (and demanding) themes of the field. Here, we consider the necessity for regulating this exchange, the possible mechanism(s) and structural elements likely involved in such regulation, and how regulatory phenomena could be perceived as changes in chemical vs. electrical coupling; an overall reflection on our collective knowledge of junctional communication is then applied to suggest new avenues of research. This article is part of a Special Issue entitled: The Communicating junctions, roles and dysfunctions. Copyright © 2012 Elsevier B.V. All rights reserved.

GAP-43 is essential for the neurotrophic effects of BDNF and positive AMPA receptor modulator S18986.

PubMed

Gupta, S K; Mishra, R; Kusum, S; Spedding, M; Meiri, K F; Gressens, P; Mani, S

2009-04-01

Positive alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor modulators include benzamide compounds that allosterically modulate AMPA glutamate receptors. These small molecules that cross the blood-brain barrier have been shown to act as a neuroprotectant by increasing the levels of endogenous brain-derived neurotrophic factor (BDNF). Positive AMPA receptor modulators have also been shown to increase the levels of growth-associated protein-43 (GAP-43). GAP-43 plays a major role in many aspects of neuronal function in vertebrates. The goal of this study was to determine whether GAP-43 was important in mediating the actions of positive AMPA receptor modulator (S18986) and BDNF. Using cortical cultures from GAP-43 knockout and control mice, we show that (1) GAP-43 is upregulated in response to S18986 and BDNF in control cultures; (2) this upregulation of GAP-43 is essential for mediating the neuroprotective effects of S18986 and BDNF; (3) administration of S18986 and BDNF leads to an increase in the expression of the glutamate transporters GLT-1 and GLAST that are key to limiting excitotoxic cell death and this increase in GLT-1 and GLAST expression is completely blocked in the absence of GAP-43. Taken together this study concludes that GAP-43 is an important mediator of the neurotrophic effects of S18986 and BDNF on neuronal survival and plasticity, and is essential for the success of positive AMPA receptor modulator-BDNF-based neurotrophin therapy.

Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research.

PubMed

Jinawath, Natini; Bunbanjerdsuk, Sacarin; Chayanupatkul, Maneerat; Ngamphaiboon, Nuttapong; Asavapanumas, Nithi; Svasti, Jisnuson; Charoensawan, Varodom

2016-11-22

With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases.

Pore diameter effects on phase behavior of a gas condensate in graphitic one-and two-dimensional nanopores.

PubMed

Welch, William R W; Piri, Mohammad

2016-01-01

Molecular dynamics (MD) simulations were performed on a hydrocarbon mixture representing a typical gas condensate composed mostly of methane and other small molecules with small fractions of heavier hydrocarbons, representative of mixtures found in tight shale reservoirs. The fluid was examined both in bulk and confined to graphitic nano-scale slits and pores. Numerous widths and diameters of slits and pores respectively were examined under variable pressures at 300 K in order to find conditions in which the fluid at the center of the apertures would not be affected by capillary condensation due to the oil-wet walls. For the bulk fluid, retrograde phase behavior was verified by liquid volumes obtained from Voronoi tessellations. In cases of both one and two-dimensional confinement, for the smallest apertures, heavy molecules aggregated inside the pore space and compression of the gas outside the solid structure lead to decreases in density of the confined fluid. Normal density/pressure relationships were observed for slits having gaps of above 3 nm and pores having diameters above 6 nm. At 70 bar, the minimum gap width at which the fluid could pass through the center of slits without condensation effects was predicted to be 6 nm and the corresponding diameter in pores was predicted to be 8 nm. The models suggest that in nanoscale networks involving pores smaller than these limiting dimensions, capillary condensation should significantly impede transmission of natural gases with similar composition.

Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python.

PubMed

Andrew, Audra L; Perry, Blair W; Card, Daren C; Schield, Drew R; Ruggiero, Robert P; McGaugh, Suzanne E; Choudhary, Amit; Secor, Stephen M; Castoe, Todd A

2017-05-02

Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process. However, substantial gaps remain in our understanding of coherent mechanisms and specific growth pathways that underlie these rapid and extensive shifts in organ form and function. Here we addressed these gaps by comparing gene expression in the Burmese python heart, liver, kidney, and small intestine across pre- and post-feeding time points (fasted, one day post-feeding, and four days post-feeding), and by conducting detailed analyses of molecular pathways and predictions of upstream regulatory molecules across these organ systems. Identified enriched canonical pathways and upstream regulators indicate that while downstream transcriptional responses are fairly tissue specific, a suite of core pathways and upstream regulator molecules are shared among responsive tissues. Pathways such as mTOR signaling, PPAR/LXR/RXR signaling, and NRF2-mediated oxidative stress response are significantly differentially regulated in multiple tissues, indicative of cell growth and proliferation along with coordinated cell-protective stress responses. Upstream regulatory molecule analyses identify multiple growth factors, kinase receptors, and transmembrane receptors, both within individual organs and across separate tissues. Downstream transcription factors MYC and SREBF are induced in all tissues. These results suggest that largely divergent patterns of post-feeding gene regulation across tissues are mediated by a core set of higher-level signaling molecules. Consistent enrichment of the NRF2-mediated oxidative stress response indicates this pathway may be particularly important in mediating cellular stress during such extreme regenerative growth.

Bi-diketopyrrolopyrrole (Bi-DPP) as a novel electron accepting compound in low band gap π-conjugated donor–acceptor copolymers/oligomers

PubMed Central

Ahner, Johannes; Nowotny, Jürgen; Schubert, Ulrich S.; Hager, Martin D.

2017-01-01

Abstract The synthesis and characterization of a novel 2,5-diketopyrrolo[3,4-c]pyrrole(DPP)-based accepting building block with the scheme DPP-neutral small linker-DPP (Bi-DPP) is presented, which was utilized as electron accepting moiety for low band gap π-conjugated donor–acceptor copolymers as well as for a donor–acceptor small molecule. The electron accepting moiety Bi-DPP was prepared via a novel synthetic pathway by building up two DPP moieties step by step simultaneously starting from a neutral phenyl core unit. Characterization of the synthesized oligomeric and polymeric materials via cyclic voltammetry afford LUMO energy levels from −3.49 to −3.59 eV as well as HOMO energy levels from −5.07 to −5.34 eV resulting in low energy band gaps from 1.52 to 1.81 eV. Spin coating of the prepared donor–acceptor oligomers/polymers resulted in well-defined films. Moreover, UV–vis measurements of the investigated donor–acceptor systems showed a broad absorption over the whole visible region. It is demonstrated that Bi-DPP as an electron accepting moiety in donor–acceptor systems offer potential properties for organic solar cell devices. PMID:29491794

Cell-specific expression of connexins and evidence of restricted gap junctional coupling between glial cells and between neurons.

PubMed

Rash, J E; Yasumura, T; Dudek, F E; Nagy, J I

2001-03-15

The transmembrane connexin proteins of gap junctions link extracellularly to form channels for cell-to-cell exchange of ions and small molecules. Two primary hypotheses of gap junction coupling in the CNS are the following: (1) generalized coupling occurs between neurons and glia, with some connexins expressed in both neurons and glia, and (2) intercellular junctional coupling is restricted to specific coupling partners, with different connexins expressed in each cell type. There is consensus that gap junctions link neurons to neurons and astrocytes to oligodendrocytes, ependymocytes, and other astrocytes. However, unresolved are the existence and degree to which gap junctions occur between oligodendrocytes, between oligodendrocytes and neurons, and between astrocytes and neurons. Using light microscopic immunocytochemistry and freeze-fracture replica immunogold labeling of adult rat CNS, we investigated whether four of the best-characterized CNS connexins are each present in one or more cell types, whether oligodendrocytes also share gap junctions with other oligodendrocytes or with neurons, and whether astrocytes share gap junctions with neurons. Connexin32 (Cx32) was found only in gap junctions of oligodendrocyte plasma membranes, Cx30 and Cx43 were found only in astrocyte membranes, and Cx36 was only in neurons. Oligodendrocytes shared intercellular gap junctions only with astrocytes, with each oligodendrocyte isolated from other oligodendrocytes except via astrocyte intermediaries. Finally, neurons shared gap junctions only with other neurons and not with glial cells. Thus, the different cell types of the CNS express different connexins, which define separate pathways for neuronal versus glial gap junctional communication.

Vibrational renormalisation of the electronic band gap in hexagonal and cubic ice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engel, Edgar A., E-mail: eae32@cam.ac.uk; Needs, Richard J.; Monserrat, Bartomeu

2015-12-28

Electron-phonon coupling in hexagonal and cubic water ice is studied using first-principles quantum mechanical methods. We consider 29 distinct hexagonal and cubic ice proton-orderings with up to 192 molecules in the simulation cell to account for proton-disorder. We find quantum zero-point vibrational corrections to the minimum electronic band gaps ranging from −1.5 to −1.7 eV, which leads to improved agreement between calculated and experimental band gaps. Anharmonic nuclear vibrations play a negligible role in determining the gaps. Deuterated ice has a smaller band-gap correction at zero-temperature of −1.2 to −1.4 eV. Vibrations reduce the differences between the electronic band gapsmore » of different proton-orderings from around 0.17 eV to less than 0.05 eV, so that the electronic band gaps of hexagonal and cubic ice are almost independent of the proton-ordering when quantum nuclear vibrations are taken into account. The comparatively small reduction in the band gap over the temperature range 0 − 240 K of around 0.1 eV does not depend on the proton ordering, or whether the ice is protiated or deuterated, or hexagonal, or cubic. We explain this in terms of the atomistic origin of the strong electron-phonon coupling in ice.« less

Electronic structure changes during the on-surface synthesis of nitrogen-doped chevron-shaped graphene nanoribbons

NASA Astrophysics Data System (ADS)

Maaß, Friedrich; Utecht, Manuel; Stremlau, Stephan; Gille, Marie; Schwarz, Jutta; Hecht, Stefan; Klamroth, Tillmann; Tegeder, Petra

2017-07-01

Utilizing suitable precursor molecules, a thermally activated and surface-assisted synthesis results in the formation of defect-free graphene nanoribbons (GNRs), which exhibit electronic properties that are not present in extended graphene. Most importantly, they have a band gap in the order of a few electron volts, depending on the nanoribbon width. In this study, we investigate the electronic structure changes during the formation of GNRs, nitrogen-doped (singly and doubly N-doped) as well as non-N-doped chevron-shaped CGNRs on Au(111). Thus we determine the optical gaps of the precursor molecules, the intermediate nonaromatic polymers, and finally the aromatic GNRs, using high-resolution electron energy loss spectroscopy and density functional theory calculations. As expected, we find no influence of N-doping on the size of the optical gaps. The gap of the precursor molecules is around 4.5 eV. Polymerization leads to a reduction of the gap to a value of 3.2 eV due to elongation and thus enhanced delocalization. The CGNRs exhibit a band gap of 2.8 eV, thus the gap is further reduced in the nanoribbons, since they exhibit an extended delocalized π -electron system.

Fixed-Gap Tunnel Junction for Reading DNA Nucleotides

PubMed Central

2015-01-01

Previous measurements of the electronic conductance of DNA nucleotides or amino acids have used tunnel junctions in which the gap is mechanically adjusted, such as scanning tunneling microscopes or mechanically controllable break junctions. Fixed-junction devices have, at best, detected the passage of whole DNA molecules without yielding chemical information. Here, we report on a layered tunnel junction in which the tunnel gap is defined by a dielectric layer, deposited by atomic layer deposition. Reactive ion etching is used to drill a hole through the layers so that the tunnel junction can be exposed to molecules in solution. When the metal electrodes are functionalized with recognition molecules that capture DNA nucleotides via hydrogen bonds, the identities of the individual nucleotides are revealed by characteristic features of the fluctuating tunnel current associated with single-molecule binding events. PMID:25380505

Investigation of the mechanism for penetration of low density lipoprotein into the arterial wall

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Zyktin, A. A.; Slepchenkov, M. M.

2018-02-01

Currently, the pathology of the cardiovascular system is an extremely urgent problem of fundamental and clinical medicine. These diseases are caused, mainly, by atherosclerotic changes in the wall of blood vessels. The predominant role in the development of atherosclerosis is attributed to the penetration of various kinds of lipoproteins into the arterial intima. In this paper, we in silico investigated the dynamics of the penetration of low density lipoprotein (LDL) through the intercellular gap using molecular modeling methods. The simulation was carried out in the GROMACS software package using a coarse-grained MARTINI model. During investigation we carried out the LDL self-assembly for the first time. The coarse-grained model of LDL was collected from the following molecules: POPC (phosphatidylcholine) - 630 molecules, LPC (lysophosphatidylcholine) - 80 molecules CHOL (cholesterol) - 600 molecules CHYO (cholesteryl oleate) - 1600 molecules TOG (glycerol trioleate) 180 Molecules. The coarse-grained model of the intercellular endothelial gap was based on a model of lipid bilayer consisting of DPPC phospholipids and cholesterol in a percentage ratio of 70% and 30%, respectively. Based on the obtained results, we can predict the mechanism of LDL diffusion. Lipoproteins can be deformed so as to pass through narrow gaps. Our investigations open the way for the research of the behavior dynamics of LDL moving with the blood flow rate when interacting with the intercellular gaps of the endothelial layer of the vessel inner wall.

Two Classes of Gap Junction Channels Mediate Soma-Germline Interactions Essential for Germline Proliferation and Gametogenesis in Caenorhabditis elegans

PubMed Central

Starich, Todd A.; Hall, David H.; Greenstein, David

2014-01-01

In all animals examined, somatic cells of the gonad control multiple biological processes essential for germline development. Gap junction channels, composed of connexins in vertebrates and innexins in invertebrates, permit direct intercellular communication between cells and frequently form between somatic gonadal cells and germ cells. Gap junctions comprise hexameric hemichannels in apposing cells that dock to form channels for the exchange of small molecules. Here we report essential roles for two classes of gap junction channels, composed of five innexin proteins, in supporting the proliferation of germline stem cells and gametogenesis in the nematode Caenorhabditis elegans. Transmission electron microscopy of freeze-fracture replicas and fluorescence microscopy show that gap junctions between somatic cells and germ cells are more extensive than previously appreciated and are found throughout the gonad. One class of gap junctions, composed of INX-8 and INX-9 in the soma and INX-14 and INX-21 in the germ line, is required for the proliferation and differentiation of germline stem cells. Genetic epistasis experiments establish a role for these gap junction channels in germline proliferation independent of the glp-1/Notch pathway. A second class of gap junctions, composed of somatic INX-8 and INX-9 and germline INX-14 and INX-22, is required for the negative regulation of oocyte meiotic maturation. Rescue of gap junction channel formation in the stem cell niche rescues germline proliferation and uncovers a later channel requirement for embryonic viability. This analysis reveals gap junctions as a central organizing feature of many soma–germline interactions in C. elegans. PMID:25195067

Giant surfactants provide a versatile platform for sub-10-nm nanostructure engineering

PubMed Central

Yu, Xinfei; Yue, Kan; Hsieh, I-Fan; Li, Yiwen; Dong, Xue-Hui; Liu, Chang; Xin, Yu; Wang, Hsiao-Fang; Shi, An-Chang; Newkome, George R.; Chen, Er-Qiang; Zhang, Wen-Bin; Cheng, Stephen Z. D.

2013-01-01

The engineering of structures across different length scales is central to the design of novel materials with controlled macroscopic properties. Herein, we introduce a unique class of self-assembling materials, which are built upon shape- and volume-persistent molecular nanoparticles and other structural motifs, such as polymers, and can be viewed as a size-amplified version of the corresponding small-molecule counterparts. Among them, “giant surfactants” with precise molecular structures have been synthesized by “clicking” compact and polar molecular nanoparticles to flexible polymer tails of various composition and architecture at specific sites. Capturing the structural features of small-molecule surfactants but possessing much larger sizes, giant surfactants bridge the gap between small-molecule surfactants and block copolymers and demonstrate a duality of both materials in terms of their self-assembly behaviors. The controlled structural variations of these giant surfactants through precision synthesis further reveal that their self-assemblies are remarkably sensitive to primary chemical structures, leading to highly diverse, thermodynamically stable nanostructures with feature sizes around 10 nm or smaller in the bulk, thin-film, and solution states, as dictated by the collective physical interactions and geometric constraints. The results suggest that this class of materials provides a versatile platform for engineering nanostructures with sub-10-nm feature sizes. These findings are not only scientifically intriguing in understanding the chemical and physical principles of the self-assembly, but also technologically relevant, such as in nanopatterning technology and microelectronics. PMID:23716680

Analytical vacuum force, atmospheric pressure dispute

NASA Astrophysics Data System (ADS)

Yongquan, Han

Typically, the gap gas molecules is 10-9 m, since the center speed of the tornado is over 100 m / sec, it divided by the speed of a tornado, the gap of the gas molecules becomes 10-11m. Equivalent to the gap when there is no tornado that the gas molecules allow radiation to pass through, equivalent to the gap is reduced gas molecules 100 times by a tornado. There is no change in the Earth's radiate, the Earth's radiation is reduced to one percent of the original intensity by the radiation through the tornado periphery into the center of the tornado. According to the APS Division of Nuclear Physics in APS -2013 Fall Meeting - Event - Gravitational radiation theory http://meetings.aps.org/Meeting/DNP13/Session/FB.8, which I published, the gravity will br reduced to the original gravity percentage one. Waterspout by the Earth's gravity to become the original one percent. Cause the external of the tornadoes atmospheric pressure is constant, the height waterspout should support column height atmospheric pressure is 100 times,that height waterspout may reach nearly kilometers.

Electronic spectra from TDDFT and machine learning in chemical space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramakrishnan, Raghunathan; Hartmann, Mia; Tapavicza, Enrico

Due to its favorable computational efficiency, time-dependent (TD) density functional theory (DFT) enables the prediction of electronic spectra in a high-throughput manner across chemical space. Its predictions, however, can be quite inaccurate. We resolve this issue with machine learning models trained on deviations of reference second-order approximate coupled-cluster (CC2) singles and doubles spectra from TDDFT counterparts, or even from DFT gap. We applied this approach to low-lying singlet-singlet vertical electronic spectra of over 20 000 synthetically feasible small organic molecules with up to eight CONF atoms. The prediction errors decay monotonously as a function of training set size. For amore » training set of 10 000 molecules, CC2 excitation energies can be reproduced to within +/- 0.1 eV for the remaining molecules. Analysis of our spectral database via chromophore counting suggests that even higher accuracies can be achieved. Based on the evidence collected, we discuss open challenges associated with data-driven modeling of high-lying spectra and transition intensities.« less

Size-scaling behaviour of the electronic polarizability of one-dimensional interacting systems

NASA Astrophysics Data System (ADS)

Chiappe, G.; Louis, E.; Vergés, J. A.

2018-05-01

Electronic polarizability of finite chains is accurately calculated from the total energy variation of the system produced by small but finite static electric fields applied along the chain direction. Normalized polarizability, that is, polarizability divided by chain length, diverges as the second power of length for metallic systems but approaches a constant value for insulating systems. This behaviour provides a very convenient way to characterize the wave-function malleability of finite systems as it avoids the need of attaching infinite contacts to the chain ends. Hubbard model calculations at half filling show that the method works for a small U  =  1 interaction value that corresponds to a really small spectral gap of 0.005 (hopping t  =  ‑1 is assumed). Once successfully checked, the method has been applied to the long-range hopping model of Gebhard and Ruckenstein showing 1/r hopping decay (Gebhard and Ruckenstein 1992 Phys. Rev. Lett. 68 244; Gebhard et al 1994 Phys. Rev. B 49 10926). Metallicity for U values below the reported metal-insulator transition is obtained but the surprise comes for U values larger than the critical one (when a gap appears in the spectral density of states) because a steady increase of the normalized polarizability with size is obtained. This critical size-scaling behaviour can be understood as corresponding to a molecule which polarizability is unbounded. We have checked that a real transfer of charge from one chain end to the opposite occurs as a response to very small electric fields in spite of the existence of a large gap of the order of U for one-particle excitations. Finally, ab initio quantum chemistry calculations of realistic poly-acetylene chains prove that the occurrence of such critical behaviour in real systems is unlikely.

Light-Driven Nano-oscillators for Label-Free Single-Molecule Monitoring of MicroRNA.

PubMed

Chen, Zixuan; Peng, Yujiao; Cao, Yue; Wang, Hui; Zhang, Jian-Rong; Chen, Hong-Yuan; Zhu, Jun-Jie

2018-06-13

Here, we present a mapping tool based on individual light-driven nano-oscillators for label-free single-molecule monitoring of microRNA. This design uses microRNA as a single-molecule damper for nano-oscillators by forming a rigid dual-strand structure in the gap between nano-oscillators and the immobilized surface. The ultrasensitive detection is attributed to comparable dimensions of the gap and microRNA. A developed surface plasmon-coupled scattering imaging technology enables us to directly measure the real-time gap distance vibration of multiple nano-oscillators with high accuracy and fast dynamics. High-level and low-level states of the oscillation amplitude indicate melting and hybridization statuses of microRNA. Lifetimes of two states reveal that the hybridization rate of microRNA is determined by the three-dimensional diffusion. This imaging technique contributes application potentials in a single-molecule detection and nanomechanics study.

Systematic design of active spaces for multi-reference calculations of singlet-triplet gaps of organic diradicals, with benchmarks against doubly electron-attached coupled-cluster data

NASA Astrophysics Data System (ADS)

Stoneburner, Samuel J.; Shen, Jun; Ajala, Adeayo O.; Piecuch, Piotr; Truhlar, Donald G.; Gagliardi, Laura

2017-10-01

Singlet-triplet gaps in diradical organic π-systems are of interest in many applications. In this study, we calculate them in a series of molecules, including cyclobutadiene and its derivatives and cyclopentadienyl cation, by using correlated participating orbitals within the complete active space (CAS) and restricted active space (RAS) self-consistent field frameworks, followed by second-order perturbation theory (CASPT2 and RASPT2). These calculations are evaluated by comparison with the results of doubly electron-attached (DEA) equation-of-motion (EOM) coupled-cluster (CC) calculations with up to 4-particle-2-hole (4p-2h) excitations. We find active spaces that can accurately reproduce the DEA-EOMCC(4p-2h) data while being small enough to be applicable to larger organic diradicals.

A Technique for Estimating the Surface Conductivity of Single Molecules

NASA Astrophysics Data System (ADS)

Bau, Haim; Arsenault, Mark; Zhao, Hui; Purohit, Prashant; Goldman, Yale

2007-11-01

When an AC electric field at 2MHz was applied across a small gap between two metal electrodes elevated above a surface, rhodamine-phalloidin-labeled actin filaments were attracted to the gap and became suspended between the two electrodes. The variance of each filament's horizontal, lateral displacement was measured as a function of electric field intensity and position along the filament. The variance significantly decreased as the electric field intensity increased. Hypothesizing that the electric field induces electroosmotic flow around the filament that, in turn, induces drag on the filament, which appears as effective tension, we estimated the tension using a linear, Brownian dynamic model. Based on the tension, we estimated the filament's surface conductivity. Our experimental method provides a novel means for trapping and manipulating biological filaments and for probing the surface conductance and mechanical properties of single polymers.

On the chemical enhancement in SERS

NASA Astrophysics Data System (ADS)

Jensen, Lasse

2012-12-01

In Surface-enhanced Raman scattering (SERS), the Raman signal of a molecule adsorbed on a metal surface is enhanced by many orders of magnitude. This provides a "finger-print" of molecules which can be used in ultrasensitive sensing devises. Here we present a time-dependent density functional theory (TDDFT) study of the molecule-surface chemical coupling in SERS. A systematic study of the chemical enhancement (CHEM) of meta-and para-substituted pyridines interacting with a small silver cluster (Ag20) is presented. We find that the magnitude of chemical enhancement is governed to a large extent by the energy difference between the highest occupied energy level (HOMO) of the metal and the lowest unoccupied energy level (LUMO) of the molecule. A two-state approximation shows that the enhancement scales roughly as (ωX/ω¯e)4, where accent="true">ω¯e is an average excitation energy between the HOMO of the metal and the LUMO of the molecule and wX the HOMO-LUMO gap of the free molecule. Furthermore, we demonstrate that it is possible to control the CHEM enhancement by switching a dithienylethene photoswitch from its closed form to its open form. The open form of the photoswitch is found to be the strongest Raman scatterer when adsorbed on the surface whereas the opposite is found for the free molecule. This trend is explained using the simple two-state approximation.

The C9orf72 repeat expansion disrupts nucleocytoplasmic transport.

PubMed

Zhang, Ke; Donnelly, Christopher J; Haeusler, Aaron R; Grima, Jonathan C; Machamer, James B; Steinwald, Peter; Daley, Elizabeth L; Miller, Sean J; Cunningham, Kathleen M; Vidensky, Svetlana; Gupta, Saksham; Thomas, Michael A; Hong, Ingie; Chiu, Shu-Ling; Huganir, Richard L; Ostrow, Lyle W; Matunis, Michael J; Wang, Jiou; Sattler, Rita; Lloyd, Thomas E; Rothstein, Jeffrey D

2015-09-03

The hexanucleotide repeat expansion (HRE) GGGGCC (G4C2) in C9orf72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies support an HRE RNA gain-of-function mechanism of neurotoxicity, and we previously identified protein interactors for the G4C2 RNA including RanGAP1. A candidate-based genetic screen in Drosophila expressing 30 G4C2 repeats identified RanGAP (Drosophila orthologue of human RanGAP1), a key regulator of nucleocytoplasmic transport, as a potent suppressor of neurodegeneration. Enhancing nuclear import or suppressing nuclear export of proteins also suppresses neurodegeneration. RanGAP physically interacts with HRE RNA and is mislocalized in HRE-expressing flies, neurons from C9orf72 ALS patient-derived induced pluripotent stem cells (iPSC-derived neurons), and in C9orf72 ALS patient brain tissue. Nuclear import is impaired as a result of HRE expression in the fly model and in C9orf72 iPSC-derived neurons, and these deficits are rescued by small molecules and antisense oligonucleotides targeting the HRE G-quadruplexes. Nucleocytoplasmic transport defects may be a fundamental pathway for ALS and FTD that is amenable to pharmacotherapeutic intervention.

Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope

PubMed Central

Nazin, G. V.; Wu, S. W.; Ho, W.

2005-01-01

The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends. PMID:15956189

Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope.

PubMed

Nazin, G V; Wu, S W; Ho, W

2005-06-21

The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends.

Two classes of gap junction channels mediate soma-germline interactions essential for germline proliferation and gametogenesis in Caenorhabditis elegans.

PubMed

Starich, Todd A; Hall, David H; Greenstein, David

2014-11-01

In all animals examined, somatic cells of the gonad control multiple biological processes essential for germline development. Gap junction channels, composed of connexins in vertebrates and innexins in invertebrates, permit direct intercellular communication between cells and frequently form between somatic gonadal cells and germ cells. Gap junctions comprise hexameric hemichannels in apposing cells that dock to form channels for the exchange of small molecules. Here we report essential roles for two classes of gap junction channels, composed of five innexin proteins, in supporting the proliferation of germline stem cells and gametogenesis in the nematode Caenorhabditis elegans. Transmission electron microscopy of freeze-fracture replicas and fluorescence microscopy show that gap junctions between somatic cells and germ cells are more extensive than previously appreciated and are found throughout the gonad. One class of gap junctions, composed of INX-8 and INX-9 in the soma and INX-14 and INX-21 in the germ line, is required for the proliferation and differentiation of germline stem cells. Genetic epistasis experiments establish a role for these gap junction channels in germline proliferation independent of the glp-1/Notch pathway. A second class of gap junctions, composed of somatic INX-8 and INX-9 and germline INX-14 and INX-22, is required for the negative regulation of oocyte meiotic maturation. Rescue of gap junction channel formation in the stem cell niche rescues germline proliferation and uncovers a later channel requirement for embryonic viability. This analysis reveals gap junctions as a central organizing feature of many soma-germline interactions in C. elegans. Copyright © 2014 by the Genetics Society of America.

Lessons from isolable nickel(I) precursor complexes for small molecule activation.

PubMed

Yao, Shenglai; Driess, Matthias

2012-02-21

Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through density functional theory (DFT) calculations, the geometric and electronic structures of these complexes were established and their distinctive reactivity, including the unprecedented monooxygenase-like activity of a bis(μ-oxo)nickel-iron complex, was studied. The studies have further led to other heterobimetallic complexes containing a [NiO(2)M] core, which are useful for understanding the influence of the heterometal on structure-reactivity relationships. The activation of N(2)O led directly to the hydrogen-atom abstraction product bis(μ-hydroxo)nickel(II) species and prevented isolation of any intermediate. In contrast, the activation of elemental S, Se, and Te with the same nickel(I) reagent furnished activation products with superchalcogenido E(2)(-) (E is S, Se, or Te) and dichalcogenido E(2)(2-) ligand in different activation stages. The isolable supersulfidonickel(II) subunit may serve as a versatile building block for the synthesis of heterobimetallic disulfidonickel(II) complexes with a [NiS(2)M] core. In the case of white phosphorus, the P(4) molecule has been coordinated to the nickel(I) center of dinuclear β-diketiminatonickel(I) precursor complexes; however, the whole P(4) subunit is a weaker electron acceptor than the dichalcogen ligands E(2), thus remaining unreduced. This P(4) binding mode is rare and could open new doors for subsequent functionalization of P(4). Our advances in understanding how these small molecules are bound to a nickel(I) center and are activated for further transformation offer promise for designing new catalysts. These nickel-containing complexes offer exceptional potential for nickel-mediated transformations of organic molecules and as model compounds for mimicking active sites of nickel-containing metalloenzymes.

Sodium leak detection system for liquid metal cooled nuclear reactors

DOEpatents

Modarres, Dariush

1991-01-01

A light source is projected across the gap between the containment vessel and the reactor vessel. The reflected light is then analyzed with an absorption spectrometer. The presence of any sodium vapor along the optical path results in a change of the optical transmissivity of the media. Since the absorption spectrum of sodium is well known, the light source is chosen such that the sensor is responsive only to the presence of sodium molecules. The optical sensor is designed to be small and require a minimum of amount of change to the reactor containment vessel.

Sensing with Superconducting Point Contacts

PubMed Central

Nurbawono, Argo; Zhang, Chun

2012-01-01

Superconducting point contacts have been used for measuring magnetic polarizations, identifying magnetic impurities, electronic structures, and even the vibrational modes of small molecules. Due to intrinsically small energy scale in the subgap structures of the supercurrent determined by the size of the superconducting energy gap, superconductors provide ultrahigh sensitivities for high resolution spectroscopies. The so-called Andreev reflection process between normal metal and superconductor carries complex and rich information which can be utilized as powerful sensor when fully exploited. In this review, we would discuss recent experimental and theoretical developments in the supercurrent transport through superconducting point contacts and their relevance to sensing applications, and we would highlight their current issues and potentials. A true utilization of the method based on Andreev reflection analysis opens up possibilities for a new class of ultrasensitive sensors. PMID:22778630

Small-molecule intramimics of formin autoinhibition: a new strategy to target the cytoskeletal remodeling machinery in cancer cells.

PubMed

Lash, L Leanne; Wallar, Bradley J; Turner, Julie D; Vroegop, Steven M; Kilkuskie, Robert E; Kitchen-Goosen, Susan M; Xu, H Eric; Alberts, Arthur S

2013-11-15

Although the cancer cell cytoskeleton is a clinically validated target, few new strategies have emerged for selectively targeting cell division by modulating the cytoskeletal structure, particularly ways that could avoid the cardiotoxic and neurotoxic effects of current agents such as taxanes. We address this gap by describing a novel class of small-molecule agonists of the mammalian Diaphanous (mDia)-related formins, which act downstream of Rho GTPases to assemble actin filaments, and their organization with microfilaments to establish and maintain cell polarity during migration and asymmetric division. GTP-bound Rho activates mDia family members by disrupting the interaction between the DID and DAD autoregulatory domains, which releases the FH2 domain to modulate actin and microtubule dynamics. In screening for DID-DAD disruptors that activate mDia, we identified two molecules called intramimics (IMM-01 and -02) that were sufficient to trigger actin assembly and microtubule stabilization, serum response factor-mediated gene expression, cell-cycle arrest, and apoptosis. In vivo analysis of IMM-01 and -02 established their ability to slow tumor growth in a mouse xenograft model of colon cancer. Taken together, our work establishes the use of intramimics and mDia-related formins as a new general strategy for therapeutic targeting of the cytoskeletal remodeling machinery of cancer cells. ©2013 AACR

Low-Symmetry Gap Functions of Organic Superconductors

NASA Astrophysics Data System (ADS)

Mori, Takehiko

2018-04-01

Superconducting gap functions of various low-symmetry organic superconductors are investigated starting from the tight-binding energy band and the random phase approximation by numerically solving Eliashberg's equation. The obtained singlet gap function is approximately represented by an asymmetrical dx2 - y2 form, where two cosine functions are mixed in an appropriate ratio. This is usually called d + s wave, where the ratio of the two cosine functions varies from 1:1 in the two-dimensional limit to 1:0 in the one-dimensional limit. A single cosine function does not make a superconducting gap in an ideal one-dimensional conductor, but works as a relevant gap function in quasi-one-dimensional conductors with slight interchain transfer integrals. Even when the Fermi surface is composed of small pockets, the gap function is obtained supposing a globally connected elliptical Fermi surface. In such a case, we have to connect the second energy band in the second Brillouin zone. The periodicity of the resulting gap function is larger than the first Brillouin zone. This is because the susceptibility has peaks at 2kF, where the periodicity has to be twice the size of the global Fermi surface. In general, periodicity of gap function corresponds to one electron or two molecules in the real space. In the κ-phase, two axes are nonequivalent, but the exact dx2 - y2 symmetry is maintained because the diagonal transfer integral introduced to a square lattice is oriented to the node direction of the dx2 - y2 wave. By contrast, the θ-phase gap function shows considerable anisotropy because a quarter-filled square lattice has a different dxy symmetry.

Development of optical micro resonance based sensor for detection and identification of microparticles and biological agents

NASA Astrophysics Data System (ADS)

Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Schweiger, Gustav

2009-05-01

A novel emerging technique for the label-free analysis of nanoparticles including biomolecules using optical micro cavity resonance of whispering-gallery-type modes is being developed. Schemes of such a method based on microsphere melted by laser on the tip of a standard single mode fiber optical cable with a laser and free microsphere matrix have been developed. Using a calibration principal of ultra high resolution spectroscopy based on such a scheme the method is being transformed to make further development for microbial application. The sensitivity of developed schemes has been tested to refractive index changes by monitoring the magnitude of the whispering gallery modes spectral shift. Water solutions of ethanol, glucose, vitamin C and biotin have been used. Some other schemes using similar principals: stand-alone, array and matrix microsphere resonators, liquid core optical ring resonators are also being under development. The influences of the gap in whispering-gallery modes on energy coupling, resonance quality and frequency have been investigated. An optimum gap for sensing applications has been defined at the half maximum energy coupling where both the Q factor and coupling efficiency are high and the resonance frequency is little affected by the gap variation. Developed schemes have been demonstrated to be a promising technology platform for sensitive, lab-on-chip type sensor which can be used for development of diagnostic tools for different biological molecules, e.g. proteins, oligonucleotides, oligosaccharides, lipids, small molecules, viral particles, cells as well as in different experimental contexts e.g. proteomics, genomics, drug discovery, and membrane studies.

Electronic Structure and Band Gap of Fullerenes on Tungsten Surfaces: Transition from a Semiconductor to a Metal Triggered by Annealing.

PubMed

Monazami, Ehsan; McClimon, John B; Rondinelli, James; Reinke, Petra

2016-12-21

The understanding and control of molecule-metal interfaces is critical to the performance of molecular electronics and photovoltaics devices. We present a study of the interface between C 60 and W, which is a carbide-forming transition metal. The complex solid-state reaction at the interface can be exploited to adjust the electronic properties of the molecule layer. Scanning tunneling microscopy/spectroscopy measurements demonstrate the progression of this reaction from wide band gap (>2.5 eV) to metallic molecular surface during annealing from 300 to 800 K. Differential conduction maps with 10 4 scanning tunneling spectra are used to quantify the transition in the density of states and the reduction of the band gap during annealing with nanometer spatial resolution. The electronic transition is spatially homogeneous, and the surface band gap can therefore be adjusted by a targeted annealing step. The modified molecules, which we call nanospheres, are quite resistant to ripening and coalescence, unlike any other metallic nanoparticle of the same size. Densely packed C 60 and isolated C 60 molecules show the same transition in electronic structure, which confirms that the transformation is controlled by the reaction at the C 60 -W interface. Density functional theory calculations are used to develop possible reaction pathways in agreement with experimentally observed electronic structure modulation. Control of the band gap by the choice of annealing temperature is a unique route to tailoring molecular-layer electronic properties.

Current-voltage characteristics of molecular conductors: two versus three terminal

NASA Astrophysics Data System (ADS)

Damle, P.; Rakshit, T.; Paulsson, M.; Datta, S.

2002-09-01

This paper addresses the question of whether a ``rigid molecule'' (one which does not deform in an external field) used as the conducting channel in a standard three-terminal MOSFET configuration can offer any performance advantage relative to a standard silicon MOSFET. A self-consistent solution of coupled quantum transport and Poisson's equations shows that even for extremely small channel lengths (about 1 nm), a ``well-tempered'' molecular FET demands much the same electrostatic considerations as a ``well-tempered'' conventional MOSFET. In other words, we show that just as in a conventional MOSFET, the gate oxide thickness needs to be much smaller than the channel length (length of the molecule) for the gate control to be effective. Furthermore, we show that a rigid molecule with metallic source and drain contacts has a temperature independent subthreshold slope much larger than 60 mV/decade, because the metal-induced gap states in the channel prevent it from turning off abruptly. However, this disadvantage can be overcome by using semiconductor contacts because of their band-limited nature.

Molecular adsorption on graphene

NASA Astrophysics Data System (ADS)

Kong, Lingmei; Enders, Axel; Rahman, Talat S.; Dowben, Peter A.

2014-11-01

Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H2O, H2, O2, CO, NO2, NO, and NH3), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH2, An-CH3, An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene’s electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

Phylogenetic and bioinformatic analysis of gap junction-related proteins, innexins, pannexins and connexins.

PubMed

Fushiki, Daisuke; Hamada, Yasuo; Yoshimura, Ryoichi; Endo, Yasuhisa

2010-04-01

All multi-cellular animals, including hydra, insects and vertebrates, develop gap junctions, which communicate directly with neighboring cells. Gap junctions consist of protein families called connexins in vertebrates and innexins in invertebrates. Connexins and innexins have no homology in their amino acid sequence, but both are thought to have some similar characteristics, such as a tetra-membrane-spanning structure, formation of a channel by hexamer, and transmission of small molecules (e.g. ions) to neighboring cells. Pannexins were recently identified as a homolog of innexins in vertebrate genomes. Although pannexins are thought to share the function of intercellular communication with connexins and innexins, there is little information about the relationship among these three protein families of gap junctions. We phylgenetically and bioinformatically examined these protein families and other tetra-membrane-spanning proteins using a database and three analytical softwares. The clades formed by pannexin families do not belong to the species classification but do to paralogs of each member of pannexins. Amino acid sequences of pannexins are closely related to those of innexins but less to those of connexins. These data suggest that innexins and pannexins have a common origin, but the relationship between innexins/pannexins and connexins is as slight as that of other tetra-membrane-spanning members.

Drug discovery and development for rare genetic disorders.

PubMed

Sun, Wei; Zheng, Wei; Simeonov, Anton

2017-09-01

Approximately 7,000 rare diseases affect millions of individuals in the United States. Although rare diseases taken together have an enormous impact, there is a significant gap between basic research and clinical interventions. Opportunities now exist to accelerate drug development for the treatment of rare diseases. Disease foundations and research centers worldwide focus on better understanding rare disorders. Here, the state-of-the-art drug discovery strategies for small molecules and biological approaches for orphan diseases are reviewed. Rare diseases are usually genetic diseases; hence, employing pharmacogenetics to develop treatments and using whole genome sequencing to identify the etiologies for such diseases are appropriate strategies to exploit. Beginning with high throughput screening of small molecules, the benefits and challenges of target-based and phenotypic screens are discussed. Explanations and examples of drug repurposing are given; drug repurposing as an approach to quickly move programs to clinical trials is evaluated. Consideration is given to the category of biologics which include gene therapy, recombinant proteins, and autologous transplants. Disease models, including animal models and induced pluripotent stem cells (iPSCs) derived from patients, are surveyed. Finally, the role of biomarkers in drug discovery and development, as well as clinical trials, is elucidated. © 2017 Wiley Periodicals, Inc.

Reducing the efficiency-stability-cost gap of organic photovoltaics with highly efficient and stable small molecule acceptor ternary solar cells

NASA Astrophysics Data System (ADS)

Baran, Derya; Ashraf, Raja Shahid; Hanifi, David A.; Abdelsamie, Maged; Gasparini, Nicola; Röhr, Jason A.; Holliday, Sarah; Wadsworth, Andrew; Lockett, Sarah; Neophytou, Marios; Emmott, Christopher J. M.; Nelson, Jenny; Brabec, Christoph J.; Amassian, Aram; Salleo, Alberto; Kirchartz, Thomas; Durrant, James R.; McCulloch, Iain

2017-03-01

Technological deployment of organic photovoltaic modules requires improvements in device light-conversion efficiency and stability while keeping material costs low. Here we demonstrate highly efficient and stable solar cells using a ternary approach, wherein two non-fullerene acceptors are combined with both a scalable and affordable donor polymer, poly(3-hexylthiophene) (P3HT), and a high-efficiency, low-bandgap polymer in a single-layer bulk-heterojunction device. The addition of a strongly absorbing small molecule acceptor into a P3HT-based non-fullerene blend increases the device efficiency up to 7.7 +/- 0.1% without any solvent additives. The improvement is assigned to changes in microstructure that reduce charge recombination and increase the photovoltage, and to improved light harvesting across the visible region. The stability of P3HT-based devices in ambient conditions is also significantly improved relative to polymer:fullerene devices. Combined with a low-bandgap donor polymer (PBDTTT-EFT, also known as PCE10), the two mixed acceptors also lead to solar cells with 11.0 +/- 0.4% efficiency and a high open-circuit voltage of 1.03 +/- 0.01 V.

The trap DOS in small molecule organic semiconductors: A quantitative comparison of thin-film transistors with single crystals

NASA Astrophysics Data System (ADS)

Kalb, Wolfgang; Haas, Simon; Pernstich, Kurt; Mathis, Thomas; Batlogg, Bertram

2010-03-01

Our study shows that it is possible to reach one of the ultimate goals of organic electronics: organic field-effect transistors can be produced with trap densities as low as in the bulk of single crystals. Several analytical methods to calculate the spectral density of localized states in the band gap (trap DOS) from measured data were used to clarify, if the different methods lead to similar results. We then compared quantitatively trap DOS information from the literature, correcting for differences due to different calculation methods. In the bulk of single crystals the trap DOS is lower by several orders of magnitude than in thin films. The compilation of all data strongly suggests that structural defects at grain boundaries are the main cause of ``fast'' traps in TFT's made with vacuum-evaporated pentacene. For high-performance transistors made with small molecule semiconductors such as rubrene it is essential to reduce the dipolar disorder caused by water adsorbed on the gate dielectric. We will discuss to what degree band broadening due to the thermal fluctuations of the intermolecular transfer integral is reflected in the trap DOS very close (<0.15 eV) to the mobility edge.

[Effects of forest gap size and within-gap position on the microclimate in Pinus koraiensis-dominated broadleaved mixed forest].

PubMed

Feng, Jing; Duan, Wen-Biao; Chen, Li-Xin

2012-07-01

HOBO automatic weather stations were installed in the central parts and at the south, north, east, and west edges of large, medium, and small gaps in a Pinus koraiensis-dominated broadleaved mixed forest in Xiaoxing' anling Mountains to measure the air temperature, relative humidity, and photosynthetic photon flux density (PPFD) in these locations and the total radiation and precipitation in the gap centres from June to September 2010, taking the closed forest stand and open field as the controls. The differences in the microclimate between various size forest gaps and between the gap centers and their edges as well as the variations of the microclimatic factors over time were analyzed, and the effects of sunny and overcast days on the diurnal variations of the microclimatic factors within forest gaps were compared, aimed to offer basic data and practice reference for gap regeneration and sustainable management of Pinus koraiensis-dominated broadleaved mixed forest. The PPFD was decreased in the order of large gap, medium gap, and small gap. For the same gaps, the PPFD in gap centre was greater than that in gap edge. The mean monthly air temperature and total radiation in gap centres were declined in the sequence of July, June, August, and September, and the amplitudes of the two climatic factors were decreased in the order of open field, large gap, medium gap, small gap, and closed forest stand. The mean monthly relative humidity in gap centres dropped in the order of August, July, September, and June, and the amplitude of this climatic factor was decreased in the sequence of closed forest stand, small gap, medium gap, large gap, and open field. The total and monthly precipitations for the three different size gaps and open field during measurement period generally decreased in the order of open field, large gap, medium gap, small gap, and closed forest stand. In sunny days, the variations of PPFD, air temperature, and relative humidity were greater in large gap than in small gap, but in overcast days, it was in opposite.

The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.

PubMed

Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

2014-09-01

In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree ) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge ). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree . These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. © 2014 The Authors. FEBS Journal published by John Wiley & Sons Ltd on behalf of FEBS.

Optimal width of quasicrystalline slabs of dielectric cylinders to microwave radiation transmission contrast

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andueza, Ángel; Sevilla, Joaquín; Smart Cities Institute, Universidad Pública de Navarra, 31006 Pamplona

2016-08-28

Light confinement induced by resonant states in aperiodic photonic structures is interesting for many applications. A particular case of these resonances can be found in 2D quasicrystalline arrangements of dielectric cylinders. These systems present a rather isotropic band gap as well as isolated in-gap photonic states (as a result of spatially localized resonances). These states are built by high symmetry polygonal clusters that can be regarded as photonic molecules. In this paper, we study the transmission properties of a slab of glass cylinders arranged in approximants of the decagonal quasicrystalline structure. In particular, we investigate the influence of the slabmore » width in the transmission contrast between the states and the gap. The study is both experimental and numerical in the microwave regime. We find that the best transmission contrast is found for a width of around three times the radiation wavelength. The transmission in the band gap region is mediated by the resonances of the photonic molecules. If the samples are thin enough, they become transparent except around a resonance of the photonic molecule which reflects the incoming light.« less

Largely Enhanced Single-molecule Fluorescence in Plasmonic Nanogaps formed by Hybrid Silver Nanostructures

PubMed Central

Zhang, Jian; Lakowicz, Joseph R.

2013-01-01

It has been suggested that narrow gaps between metallic nanostructures can be practical for producing large field enhancement. We design a hybrid silver nanostructure geometry in which fluorescent emitters are sandwiched between silver nanoparticles and silver island film (SIF). A desired number of polyelectrolyte layers are deposited on the SIF surface before the self-assembly of a second silver nanoparticle layer. Layer-by-layer configuration provides a well-defined dye position. It allows us to study the photophyical behaviors of fluorophores in the resulting gap at the single molecule level. The enhancement factor of a fluorophore located in the gap is much higher than those on silver surfaces alone and on glass. These effects may be used for increased detectability of single molecules bound to surfaces which contain metallic structures for either biophysical studies or high sensitivity assays. PMID:23373787

Molecular targets for small-molecule modulators of circadian clocks

PubMed Central

He, Baokun; Chen, Zheng

2016-01-01

Background Circadian clocks are endogenous timing systems that regulate various aspects of mammalian metabolism, physiology and behavior. Traditional chronotherapy refers to the administration of drugs in a defined circadian time window to achieve optimal pharmacokinetic and therapeutic efficacies. In recent years, substantial efforts have been dedicated to developing novel small-molecule modulators of circadian clocks. Methods Here, we review the recent progress in the identification of molecular targets of small-molecule clock modulators and their efficacies in clock-related disorders. Specifically, we examine the clock components and regulatory factors as possible molecular targets of small molecules, and we review several key clock-related disorders as promising venues for testing the preventive/therapeutic efficacies of these small molecules. Finally, we also discuss circadian regulation of drug metabolism. Results Small molecules can modulate the period, phase and/or amplitude of the circadian cycle. Core clock proteins, nuclear hormone receptors, and clock-related kinases and other epigenetic regulators are promising molecular targets for small molecules. Through these targets small molecules exert protective effects against clock-related disorders including the metabolic syndrome, immune disorders, sleep disorders and cancer. Small molecules can also modulate circadian drug metabolism and response to existing therapeutics. Conclusion Small-molecule clock modulators target clock components or diverse cellular pathways that functionally impinge upon the clock. Target identification of new small-molecule modulators will deepen our understanding of key regulatory nodes in the circadian network. Studies of clock modulators will facilitate their therapeutic applications, alone or in combination, for clock-related diseases. PMID:26750111

Shift in the equilibrium between on and off states of the allosteric switch in Ras-GppNHp affected by small molecules and bulk solvent composition.

PubMed

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-07

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the "ordered off" state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-β. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-31

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) canmore » selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.« less

Ringed Structures of the HD 163296 Protoplanetary Disk Revealed by ALMA

NASA Astrophysics Data System (ADS)

Isella, Andrea; Guidi, Greta; Testi, Leonardo; Liu, Shangfei; Li, Hui; Li, Shengtai; Weaver, Erik; Boehler, Yann; Carperter, John M.; De Gregorio-Monsalvo, Itziar; Manara, Carlo F.; Natta, Antonella; Pérez, Laura M.; Ricci, Luca; Sargent, Anneila; Tazzari, Marco; Turner, Neal

2016-12-01

We present Atacama Large Millimeter and Submillimeter Array observations of the protoplanetary disk around the Herbig Ae star HD 163296 that trace the spatial distribution of millimeter-sized particles and cold molecular gas on spatial scales as small as 25 astronomical units (A.U.). The image of the disk recorded in the 1.3 mm continuum emission reveals three dark concentric rings that indicate the presence of dust depleted gaps at about 60, 100, and 160 A.U. from the central star. The maps of the 12CO, 13CO, and C 18O J =2 -1 emission do not show such structures but reveal a change in the slope of the radial intensity profile across the positions of the dark rings in the continuum image. By comparing the observations with theoretical models for the disk emission, we find that the density of CO molecules is reduced inside the middle and outer dust gaps. However, in the inner ring there is no evidence of CO depletion. From the measurements of the dust and gas densities, we deduce that the gas-to-dust ratio varies across the disk and, in particular, it increases by at least a factor 5 within the inner dust gap compared to adjacent regions of the disk. The depletion of both dust and gas suggests that the middle and outer rings could be due to the gravitational torque exerted by two Saturn-mass planets orbiting at 100 and 160 A.U. from the star. On the other hand, the inner dust gap could result from dust accumulation at the edge of a magnetorotational instability dead zone, or from dust opacity variations at the edge of the CO frost line. Observations of the dust emission at higher angular resolution and of molecules that probe dense gas are required to establish more precisely the origins of the dark rings observed in the HD 163296 disk.

Ringed Structures of the HD 163296 Protoplanetary Disk Revealed by ALMA.

PubMed

Isella, Andrea; Guidi, Greta; Testi, Leonardo; Liu, Shangfei; Li, Hui; Li, Shengtai; Weaver, Erik; Boehler, Yann; Carperter, John M; De Gregorio-Monsalvo, Itziar; Manara, Carlo F; Natta, Antonella; Pérez, Laura M; Ricci, Luca; Sargent, Anneila; Tazzari, Marco; Turner, Neal

2016-12-16

We present Atacama Large Millimeter and Submillimeter Array observations of the protoplanetary disk around the Herbig Ae star HD 163296 that trace the spatial distribution of millimeter-sized particles and cold molecular gas on spatial scales as small as 25 astronomical units (A.U.). The image of the disk recorded in the 1.3 mm continuum emission reveals three dark concentric rings that indicate the presence of dust depleted gaps at about 60, 100, and 160 A.U. from the central star. The maps of the ^{12}CO, ^{13}CO, and C^{18}O J=2-1 emission do not show such structures but reveal a change in the slope of the radial intensity profile across the positions of the dark rings in the continuum image. By comparing the observations with theoretical models for the disk emission, we find that the density of CO molecules is reduced inside the middle and outer dust gaps. However, in the inner ring there is no evidence of CO depletion. From the measurements of the dust and gas densities, we deduce that the gas-to-dust ratio varies across the disk and, in particular, it increases by at least a factor 5 within the inner dust gap compared to adjacent regions of the disk. The depletion of both dust and gas suggests that the middle and outer rings could be due to the gravitational torque exerted by two Saturn-mass planets orbiting at 100 and 160 A.U. from the star. On the other hand, the inner dust gap could result from dust accumulation at the edge of a magnetorotational instability dead zone, or from dust opacity variations at the edge of the CO frost line. Observations of the dust emission at higher angular resolution and of molecules that probe dense gas are required to establish more precisely the origins of the dark rings observed in the HD 163296 disk.

Recent advances in developing small molecules targeting RNA.

PubMed

Guan, Lirui; Disney, Matthew D

2012-01-20

RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.

Control of neuronal morphology and connectivity: emerging developmental roles for gap junctional proteins.

PubMed

Baker, Michael W; Macagno, Eduardo R

2014-04-17

Recent evidence indicates that gap junction (GJ) proteins can play a critical role in controlling neuronal connectivity as well as cell morphology in the developing nervous system. GJ proteins may function analogously to cell adhesion molecules, mediating cellular recognition and selective neurite adhesion. Moreover, during synaptogenesis electrical synapses often herald the later establishment of chemical synapses, and thus may help facilitate activity-dependent sculpting of synaptic terminals. Recent findings suggest that the morphology and connectivity of embryonic leech neurons are fundamentally organized by the type and perhaps location of the GJ proteins they express. For example, ectopic expression in embryonic leech neurons of certain innexins that define small GJ-linked networks of cells leads to the novel coupling of the expressing cell into that network. Moreover, gap junctions appear to mediate interactions among homologous neurons that modulate process outgrowth and stability. We propose that the selective formation of GJs between developing neurons and perhaps glial cells in the CNS helps orchestrate not only cellular synaptic connectivity but also can have a pronounced effect on the arborization and morphology of those cells involved. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Spin Contamination Error in Optimized Geometry of Singlet Carbene (1A1) by Broken-Symmetry Method

NASA Astrophysics Data System (ADS)

Kitagawa, Yasutaka; Saito, Toru; Nakanishi, Yasuyuki; Kataoka, Yusuke; Matsui, Toru; Kawakami, Takashi; Okumura, Mitsutaka; Yamaguchi, Kizashi

2009-10-01

Spin contamination errors of a broken-symmetry (BS) method in optimized structural parameters of the singlet methylene (1A1) molecule are quantitatively estimated for the Hartree-Fock (HF) method, post-HF methods (CID, CCD, MP2, MP3, MP4(SDQ)), and a hybrid DFT (B3LYP) method. For the purpose, the optimized geometry by the BS method is compared with that of an approximate spin projection (AP) method. The difference between the BS and the AP methods is about 10-20° in the HCH angle. In order to examine the basis set dependency of the spin contamination error, calculated results by STO-3G, 6-31G*, and 6-311++G** are compared. The error depends on the basis sets, but the tendencies of each method are classified into two types. Calculated energy splitting values between the triplet and the singlet states (ST gap) indicate that the contamination of the stable triplet state makes the BS singlet solution stable and the ST gap becomes small. The energy order of the spin contamination error in the ST gap is estimated to be 10-1 eV.

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

Simulation and fabrication of a new novel 3D injectable biosensor for high throughput genomics and proteomics in a lab-on-a-chip device.

PubMed

Esfandyarpour, Rahim; Esfandyarpour, Hesaam; Harris, James S; Davis, Ronald W

2013-11-22

Biosensors are used for the detection of biochemical molecules such as proteins and nucleic acids. Traditional techniques, such as enzyme-linked immuno-sorbent assay (ELISA), are sensitive but require several hours to yield a result and usually require the attachment of a fluorophore molecule to the target molecule. Micromachined biosensors that employ electrical detection are now being developed. Here we describe one such device, which is ultrasensitive, real-time, label free and localized. It is called the nanoneedle biosensor and shows promise to overcome some of the current limitations of biosensors. The key element of this device is a 10 nm wide annular gap at the end of the needle, which is the sensitive part of the sensor. The total diameter of the sensor is about 100 nm. Any change in the population of molecules in this gap results in a change of impedance across the gap. Single molecule detection should be possible because the sensory part of the sensor is in the range of bio-molecules of interest. To increase throughput we can flow the solution containing the target molecules over an array of such structures, each with its own integrated read-out circuitry to allow 'real-time' detection (i.e. several minutes) of label free molecules without sacrificing sensitivity. To fabricate the arrays we used electron beam lithography together with associated pattern transfer techniques. Preliminary measurements on individual needle structures in water are consistent with the design. Since the proposed sensor has a rigid nano-structure, this technology, once fully developed, could ultimately be used to directly monitor protein quantities within a single living cell, an application that would have significant utility for drug screening and studying various intracellular signaling pathways.

Simulation and fabrication of a new novel 3D injectable biosensor for high throughput genomics and proteomics in a lab-on-a-chip device

NASA Astrophysics Data System (ADS)

Esfandyarpour, Rahim; Esfandyarpour, Hesaam; Harris, James S.; Davis, Ronald W.

2013-11-01

Biosensors are used for the detection of biochemical molecules such as proteins and nucleic acids. Traditional techniques, such as enzyme-linked immuno-sorbent assay (ELISA), are sensitive but require several hours to yield a result and usually require the attachment of a fluorophore molecule to the target molecule. Micromachined biosensors that employ electrical detection are now being developed. Here we describe one such device, which is ultrasensitive, real-time, label free and localized. It is called the nanoneedle biosensor and shows promise to overcome some of the current limitations of biosensors. The key element of this device is a 10 nm wide annular gap at the end of the needle, which is the sensitive part of the sensor. The total diameter of the sensor is about 100 nm. Any change in the population of molecules in this gap results in a change of impedance across the gap. Single molecule detection should be possible because the sensory part of the sensor is in the range of bio-molecules of interest. To increase throughput we can flow the solution containing the target molecules over an array of such structures, each with its own integrated read-out circuitry to allow ‘real-time’ detection (i.e. several minutes) of label free molecules without sacrificing sensitivity. To fabricate the arrays we used electron beam lithography together with associated pattern transfer techniques. Preliminary measurements on individual needle structures in water are consistent with the design. Since the proposed sensor has a rigid nano-structure, this technology, once fully developed, could ultimately be used to directly monitor protein quantities within a single living cell, an application that would have significant utility for drug screening and studying various intracellular signaling pathways.

Minding the Gap: Synthetic Strategies for Tuning the Energy Gap in Conjugated Molecules

ERIC Educational Resources Information Center

Christensen, Dana; Cohn, Pamela G.

2016-01-01

While structure-property relationships are commonly developed in applications of physical organic chemistry to real-world problems at the graduate level, they have not been generally emphasized in the undergraduate chemistry curriculum. For instance, the ability to modify the energy gap between the highest occupied molecular orbital (HOMO) and the…

Graphene symmetry-breaking with molecular adsorbates: modeling and experiment

NASA Astrophysics Data System (ADS)

Groce, M. A.; Hawkins, M. K.; Wang, Y. L.; Cullen, W. G.; Einstein, T. L.

2012-02-01

Graphene's structure and electronic properties provide a framework for understanding molecule-substrate interactions and developing techniques for band gap engineering. Controlled deposition of molecular adsorbates can create superlattices which break the degeneracy of graphene's two-atom unit cell, opening a band gap. We simulate scanning tunneling microscopy and spectroscopy measurements for a variety of organic molecule/graphene systems, including pyridine, trimesic acid, and isonicotinic acid, based on density functional theory calculations using VASP. We also compare our simulations to ultra-high vacuum STM and STS results.

Interspecies scaling and prediction of human clearance: comparison of small- and macro-molecule drugs

PubMed Central

Huh, Yeamin; Smith, David E.; Feng, Meihau Rose

2014-01-01

Human clearance prediction for small- and macro-molecule drugs was evaluated and compared using various scaling methods and statistical analysis.Human clearance is generally well predicted using single or multiple species simple allometry for macro- and small-molecule drugs excreted renally.The prediction error is higher for hepatically eliminated small-molecules using single or multiple species simple allometry scaling, and it appears that the prediction error is mainly associated with drugs with low hepatic extraction ratio (Eh). The error in human clearance prediction for hepatically eliminated small-molecules was reduced using scaling methods with a correction of maximum life span (MLP) or brain weight (BRW).Human clearance of both small- and macro-molecule drugs is well predicted using the monkey liver blood flow method. Predictions using liver blood flow from other species did not work as well, especially for the small-molecule drugs. PMID:21892879

Small-Gap Flows

DTIC Science & Technology

1984-04-01

I TV N 4 NAVAL ARCIETUR & OFFSHORE ENGINEERING SMALL- GAP FLOWSti E 0.TUCK01 REPORT NO- M!AOL 34-1 CONTRACT NJU1-𔃾-K-0026 APRIL 1984 let.? UNIVERSMn...34’OF CALIFORNIA# BERKELEY, CA 5.1720 ft (45 642-141 SMALL- GAP FLOWS BY E. 0. TUCK REPORT No. NAUE 84-1 CONTRACT N00014-84-K-OU26 APRIL i984...34small- gap " theme.Chapters 1-4 were originally presented in the form of a lecture series in the Department of Naval Architecture and Offshore

Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule.

PubMed

Takakusagi, Yoichi; Takakusagi, Kaori; Sugawara, Fumio; Sakaguchi, Kengo

2018-01-01

Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami.

PubMed

Chikkaraddy, Rohit; Turek, V A; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F; Baumberg, Jeremy J

2018-01-10

Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 10 3 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale.

Facilities for small-molecule crystallography at synchrotron sources.

PubMed

Barnett, Sarah A; Nowell, Harriott; Warren, Mark R; Wilcox, Andrian; Allan, David R

2016-01-01

Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

Architecture and permeability of post-cytokinesis plasmodesmata lacking cytoplasmic sleeves.

PubMed

Nicolas, William J; Grison, Magali S; Trépout, Sylvain; Gaston, Amélia; Fouché, Mathieu; Cordelières, Fabrice P; Oparka, Karl; Tilsner, Jens; Brocard, Lysiane; Bayer, Emmanuelle M

2017-06-12

Plasmodesmata are remarkable cellular machines responsible for the controlled exchange of proteins, small RNAs and signalling molecules between cells. They are lined by the plasma membrane (PM), contain a strand of tubular endoplasmic reticulum (ER), and the space between these two membranes is thought to control plasmodesmata permeability. Here, we have reconstructed plasmodesmata three-dimensional (3D) ultrastructure with an unprecedented level of 3D information using electron tomography. We show that within plasmodesmata, ER-PM contact sites undergo substantial remodelling events during cell differentiation. Instead of being open pores, post-cytokinesis plasmodesmata present such intimate ER-PM contact along the entire length of the pores that no intermembrane gap is visible. Later on, during cell expansion, the plasmodesmata pore widens and the two membranes separate, leaving a cytosolic sleeve spanned by tethers whose presence correlates with the appearance of the intermembrane gap. Surprisingly, the post-cytokinesis plasmodesmata allow diffusion of macromolecules despite the apparent lack of an open cytoplasmic sleeve, forcing the reassessment of the mechanisms that control plant cell-cell communication.

Accurate adiabatic singlet-triplet gaps in atoms and molecules employing the third-order spin-flip algebraic diagrammatic construction scheme for the polarization propagator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lefrancois, Daniel; Dreuw, Andreas, E-mail: dreuw@uni-heidelberg.de; Rehn, Dirk R.

For the calculation of adiabatic singlet-triplet gaps (STG) in diradicaloid systems the spin-flip (SF) variant of the algebraic diagrammatic construction (ADC) scheme for the polarization propagator in third order perturbation theory (SF-ADC(3)) has been applied. Due to the methodology of the SF approach the singlet and triplet states are treated on an equal footing since they are part of the same determinant subspace. This leads to a systematically more accurate description of, e.g., diradicaloid systems than with the corresponding non-SF single-reference methods. Furthermore, using analytical excited state gradients at ADC(3) level, geometry optimizations of the singlet and triplet states weremore » performed leading to a fully consistent description of the systems, leading to only small errors in the calculated STGs ranging between 0.6 and 2.4 kcal/mol with respect to experimental references.« less

Systems Based Study of the Therapeutic Potential of Small Charged Molecules for the Inhibition of IL-1 Mediated Cartilage Degradation

PubMed Central

Kar, Saptarshi; Smith, David W.; Gardiner, Bruce S.; Grodzinsky, Alan J.

2016-01-01

Inflammatory cytokines are key drivers of cartilage degradation in post-traumatic osteoarthritis. Cartilage degradation mediated by these inflammatory cytokines has been extensively investigated using in vitro experimental systems. Based on one such study, we have developed a computational model to quantitatively assess the impact of charged small molecules intended to inhibit IL-1 mediated cartilage degradation. We primarily focus on the simplest possible computational model of small molecular interaction with the IL-1 system—direct binding of the small molecule to the active site on the IL-1 molecule itself. We first use the model to explore the uptake and release kinetics of the small molecule inhibitor by cartilage tissue. Our results show that negatively charged small molecules are excluded from the negatively charged cartilage tissue and have uptake kinetics in the order of hours. In contrast, the positively charged small molecules are drawn into the cartilage with uptake and release timescales ranging from hours to days. Using our calibrated computational model, we subsequently explore the effect of small molecule charge and binding constant on the rate of cartilage degradation. The results from this analysis indicate that the small molecules are most effective in inhibiting cartilage degradation if they are either positively charged and/or bind strongly to IL-1α, or both. Furthermore, our results showed that the cartilage structural homeostasis can be restored by the small molecule if administered within six days following initial tissue exposure to IL-1α. We finally extended the scope of the computational model by simulating the competitive inhibition of cartilage degradation by the small molecule. Results from this model show that small molecules are more efficient in inhibiting cartilage degradation by binding directly to IL-1α rather than binding to IL-1α receptors. The results from this study can be used as a template for the design and development of more pharmacologically effective osteoarthritis drugs, and to investigate possible therapeutic options. PMID:27977731

Antibody-enabled small-molecule drug discovery.

PubMed

Lawson, Alastair D G

2012-06-29

Although antibody-based therapeutics have become firmly established as medicines for serious diseases, the value of antibodies as tools in the early stages of small-molecule drug discovery is only beginning to be realized. In particular, antibodies may provide information to reduce risk in small-molecule drug discovery by enabling the validation of targets and by providing insights into the design of small-molecule screening assays. Moreover, antibodies can act as guides in the quest for small molecules that have the ability to modulate protein-protein interactions, which have traditionally only been considered to be tractable targets for biological drugs. The development of small molecules that have similar therapeutic effects to current biologics has the potential to benefit a broader range of patients at earlier stages of disease.

Continuous high throughput molecular adhesion based cell sorting using ridged microchannels

NASA Astrophysics Data System (ADS)

Tasadduq, Bushra; Wang, Gonghao; Alexeev, Alexander; Sarioglu, Ali Fatih; Sulchek, Todd

2016-11-01

Cell molecular interactions govern important physiological processes such as stem cell homing, inflammation and cancer metastasis. But due to a lack of effective separation technologies selective to these interactions it is challenging to specifically sort cells. Other label free separation techniques based on size, stiffness and shape do not provide enough specificity to cell type, and correlation to clinical condition. We propose a novel microfluidic device capable of high throughput molecule dependent separation of cells by flowing them through a microchannel decorated with molecule specific coated ridges. The unique aspect of this sorting design is the use of optimized gap size which is small enough to lightly squeeze the cells while flowing under the ridged part of the channel to increase the surface area for interaction between the ligand on cell surface and coated receptor molecule but large enough so that biomechanical markers, stiffness and viscoelasticity, do not dominate the cell separation mechanism. We are able to separate Jurkat cells based on its expression of PSGL-1ligand using ridged channel coated with P selectin at a flow rate of 0.045ml/min and achieve 2-fold and 5-fold enrichment of PSGL-1 positive and negative Jurkat cells respectively.

Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

PubMed

Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

2016-06-21

We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results.

Small Molecule Chemical Probes of MicroRNA Function

PubMed Central

Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R.; Disney, Matthew D.

2015-01-01

MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as strides are made to understand small molecule recognition of RNA from a fundamental perspective. PMID:25500006

FAM13A is associated with non-small cell lung cancer (NSCLC) progression and controls tumor cell proliferation and survival

PubMed Central

Heim, Lisanne; Trump, Sonja; Mittler, Susanne; Sopel, Nina; Andreev, Katerina; Ferrazzi, Fulvia; Ekici, Arif B.; Rieker, Ralf; Springel, Rebekka; Assmann, Vera L.; Lechmann, Matthias; Koch, Sonja; Engelhardt, Marina; Trufa, Denis I.; Sirbu, Horia; Hartmann, Arndt; Finotto, Susetta

2017-01-01

ABSTRACT Genome-wide association studies (GWAS) associated Family with sequence similarity 13, member A (FAM13A) with non-small cell lung cancer (NSCLC) occurrence. Here, we found increased numbers of FAM13A protein expressing cells in the tumoral region of lung tissues from a cohort of patients with NSCLC. Moreover, FAM13A inversely correlated with CTLA4 but directly correlated with HIF1α levels in the control region of these patients. Consistently, FAM13A RhoGAP was found to be associated with T cell effector molecules like HIF1α and Tbet and was downregulated in immunosuppressive CD4+CD25+Foxp3+CTLA4+ T cells. TGFβ, a tumor suppressor factor, as well as siRNA to FAM13A, suppressed both isoforms of FAM13A and inhibited tumor cell proliferation. RNA-Seq analysis confirmed this finding. Moreover, siRNA to FAM13A induced TGFβ levels. Finally, in experimental tumor cell migration, FAM13A was induced and TGFβ accelerated this process by inducing cell migration, HIF1α, and the FAM13A RhoGAP isoform. Furthermore, siRNA to FAM13A inhibited tumor cell proliferation and induced cell migration without affecting HIF1α. In conclusion, FAM13A is involved in tumor cell proliferation and downstream of TGFβ and HIF1α, FAM13A RhoGAP is associated with Th1 gene expression and lung tumor cell migration. These findings identify FAM13A as key regulator of NSCLC growth and progression. PMID:28197372

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

NASA Astrophysics Data System (ADS)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

Interaction of benzene thiol and thiolate with small gold clusters.

PubMed

Letardi, Sara; Cleri, Fabrizio

2004-06-01

We studied the interaction between benzene thiol and thiolate molecules, and gold clusters made of 1 to 3 atoms, by means of ab initio density functional theory in the local density approximation. We find that the thiolate is energetically more stable than the thiol, however the process of detachment of H from the thiol appears to be possibly mediated by the intermediate step of H chemisorption on Au. Cleavage of the S-H bond is accompanied by a 90 degrees rotation of the molecule around the S-Au bond, showing a strong steric specificity. Such a rotation is induced by the relative energy shift of the S atom p orbitals with respect to the benzene pi ring and the Au d orbitals. By analyzing the correlation of the bond energy, bond lengths, and HOMO-LUMO gap with the number of S-Au bonds, we find that the thiolate S atom appears to prefer a low-coordination condition on Au clusters. (c) 2004 American Institute of Physics.

Medium-Bandgap Small-Molecule Donors Compatible with Both Fullerene and Nonfullerene Acceptors.

PubMed

Huo, Yong; Yan, Cenqi; Kan, Bin; Liu, Xiao-Fei; Chen, Li-Chuan; Hu, Chen-Xia; Lau, Tsz-Ki; Lu, Xinhui; Sun, Chun-Lin; Shao, Xiangfeng; Chen, Yongsheng; Zhan, Xiaowei; Zhang, Hao-Li

2018-03-21

Much effort has been devoted to the development of new donor materials for small-molecule organic solar cells due to their inherent advantages of well-defined molecular weight, easy purification, and good reproducibility in photovoltaic performance. Herein, we report two small-molecule donors that are compatible with both fullerene and nonfullerene acceptors. Both molecules consist of an (E)-1,2-di(thiophen-2-yl)ethane-substituted (TVT-substituted) benzo[1,2-b:4,5-b']dithiophene (BDT) as the central unit, and two rhodanine units as the terminal electron-withdrawing groups. The central units are modified with either alkyl side chains (DRBDT-TVT) or alkylthio side chains (DRBDT-STVT). Both molecules exhibit a medium bandgap with complementary absorption and proper energy level offset with typical acceptors like PC 71 BM and IDIC. The optimized devices show a decent power conversion efficiency (PCE) of 6.87% for small-molecule organic solar cells and 6.63% for nonfullerene all small-molecule organic solar cells. Our results reveal that rationally designed medium-bandgap small-molecule donors can be applied in high-performance small-molecule organic solar cells with different types of acceptors.

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.

PubMed

Disney, Matthew D; Winkelsas, Audrey M; Velagapudi, Sai Pradeep; Southern, Mark; Fallahi, Mohammad; Childs-Disney, Jessica L

2016-06-17

The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif-small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif-small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.

Isoindigo-Based Small Molecules with Varied Donor Components for Solution-Processable Organic Field Effect Transistor Devices.

PubMed

Patil, Hemlata; Chang, Jingjing; Gupta, Akhil; Bilic, Ante; Wu, Jishan; Sonar, Prashant; Bhosale, Sheshanath V

2015-09-18

Two solution-processable small organic molecules, (E)-6,6'-bis(4-(diphenylamino)phenyl)-1,1'-bis(2-ethylhexyl)-(3,3'-biindolinylidene)-2,2'-dione (coded as S10) and (E)-6,6'-di(9H-carbazol-9-yl)-1,1'-bis(2-ethylhexyl)-(3,3'-biindolinylidene)-2,2'-dione (coded as S11) were successfully designed, synthesized and fully characterized. S10 and S11 are based on a donor-acceptor-donor structural motif and contain a common electron accepting moiety, isoindigo, along with different electron donating functionalities, triphenylamine and carbazole, respectively. Ultraviolet-visible absorption spectra revealed that the use of triphenylamine donor functionality resulted in an enhanced intramolecular charge transfer transition and reduction of optical band gap, when compared with its carbazole analogue. Both of these materials were designed to be donor semiconducting components, exerted excellent solubility in common organic solvents, showed excellent thermal stability, and their promising optoelectronic properties encouraged us to scrutinize charge-carrier mobilities using solution-processable organic field effect transistors. Hole mobilities of the order of 2.2 × 10(-4) cm²/Vs and 7.8 × 10(-3) cm²/Vs were measured using S10 and S11 as active materials, respectively.

Molecular communication and networking: opportunities and challenges.

PubMed

Nakano, Tadashi; Moore, Michael J; Wei, Fang; Vasilakos, Athanasios V; Shuai, Jianwei

2012-06-01

The ability of engineered biological nanomachines to communicate with biological systems at the molecular level is anticipated to enable future applications such as monitoring the condition of a human body, regenerating biological tissues and organs, and interfacing artificial devices with neural systems. From the viewpoint of communication theory and engineering, molecular communication is proposed as a new paradigm for engineered biological nanomachines to communicate with the natural biological nanomachines which form a biological system. Distinct from the current telecommunication paradigm, molecular communication uses molecules as the carriers of information; sender biological nanomachines encode information on molecules and release the molecules in the environment, the molecules then propagate in the environment to receiver biological nanomachines, and the receiver biological nanomachines biochemically react with the molecules to decode information. Current molecular communication research is limited to small-scale networks of several biological nanomachines. Key challenges to bridge the gap between current research and practical applications include developing robust and scalable techniques to create a functional network from a large number of biological nanomachines. Developing networking mechanisms and communication protocols is anticipated to introduce new avenues into integrating engineered and natural biological nanomachines into a single networked system. In this paper, we present the state-of-the-art in the area of molecular communication by discussing its architecture, features, applications, design, engineering, and physical modeling. We then discuss challenges and opportunities in developing networking mechanisms and communication protocols to create a network from a large number of bio-nanomachines for future applications.

Bayesian molecular design with a chemical language model

NASA Astrophysics Data System (ADS)

Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

2017-04-01

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

Bayesian molecular design with a chemical language model.

PubMed

Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

2017-04-01

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

Nanoscale volume confinement and fluorescence enhancement with double nanohole aperture

PubMed Central

Regmi, Raju; Al Balushi, Ahmed A.; Rigneault, Hervé; Gordon, Reuven; Wenger, Jérôme

2015-01-01

Diffraction ultimately limits the fluorescence collected from a single molecule, and sets an upper limit to the maximum concentration to isolate a single molecule in the detection volume. To overcome these limitations, we introduce here the use of a double nanohole structure with 25 nm gap, and report enhanced detection of single fluorescent molecules in concentrated solutions exceeding 20 micromolar. The nanometer gap concentrates the light into an apex volume down to 70 zeptoliter (10−21 L), 7000-fold below the diffraction-limited confocal volume. Using fluorescence correlation spectroscopy and time-correlated photon counting, we measure fluorescence enhancement up to 100-fold, together with local density of optical states (LDOS) enhancement of 30-fold. The distinctive features of double nanoholes combining high local field enhancement, efficient background screening and relative nanofabrication simplicity offer new strategies for real time investigation of biochemical events with single molecule resolution at high concentrations. PMID:26511149

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

PubMed Central

2017-01-01

Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 103 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale. PMID:29166033

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

NASA Astrophysics Data System (ADS)

Chikkaraddy, Rohit; Turek, V. A.; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F.; Baumberg, Jeremy J.

2018-01-01

Fabricating nanocavities in which optically-active single quantum emitters are precisely positioned, is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore, and obtain enhancements of $\\geq4\\times10^3$ with high quantum yield ($\\geq50$%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of $\\pm1.5$ nm. Our approach introduces a straightforward non-invasive way to measure and quantify confined optical modes on the nanoscale.

Plasmonic nanoantenna arrays for surface-enhanced Raman spectroscopy of lipid molecules embedded in a bilayer membrane.

PubMed

Kühler, Paul; Weber, Max; Lohmüller, Theobald

2014-06-25

We demonstrate a strategy for surface-enhanced Raman spectroscopy (SERS) of supported lipid membranes with arrays of plasmonic nanoantennas. Colloidal lithography refined with plasma etching is used to synthesize arrays of triangular shaped gold nanoparticles. Reducing the separation distance between the triangle tips leads to plasmonic coupling and to a strong enhancement of the electromagnetic field in the nanotriangle gap. As a result, the Raman scattering intensity of molecules that are located at this plasmonic "hot-spot" can be increased by several orders of magnitude. The nanoantenna array is then embedded with a supported phospholipid membrane which is fluid at room temperature and spans the antenna gap. This configuration offers the advantage that molecules that are mobile within the bilayer membrane can enter the "hot-spot" region via diffusion and can therefore be measured by SERS without static entrapment or adsorption of the molecules to the antenna itself.

Theoretical and experimental studies of the electronic structure of the Mo3(Micro3-0)(Micro3-OR)(Micro-OR)3(OR)6 type of triangulo metal atom cluster compound

NASA Astrophysics Data System (ADS)

Chisholm, M. H.; Cotton, F. A.; Fang, A.; Kober, E. C.

1983-09-01

The electronic structure of a Mo3(Mu sub 3-0) (Mu sub 3-OR) (Mu sub 2-OR)3(OR)6 molecule with R = H, and C3v symmetry, which serves as a model for real molecules in which R = H CH2C(CH)3 or CH(CH3)2 has been calculated by the molecular orbital method of Hall and Fenske. The calculations have been performed not only on the entire molecule, but on the Mo3(12+), Mo3O(OH)(9+) and Mo3O(OH)4(6+) fragments and the metal-metal bonding tracked through these successive stages by the ''clusters in molecules' formalism. In the full molecule, the HOMO is an e orbital that carries most of the e-type M-M bonding, while the a1-type is carried by two MO's, one of which is quite stable. The LUMO is also an e type orbital and the HOMO-LUMO gap is small (ca. 1.5 eV). It is predicted that the Mo3O(OR)10 molecules of this type will have readily accessible redox chemistry in which both oxidation and reduction steps might be slowed or irreversible judging by the character of the HOMO and LUMO of the Mo3O(OR)10 molecule. Experimental observations on Mo3O(ONe)10, Ne = CH2C(CH3)3, are in harmony with this. In addition, the absorption spectrum of Mo3O(ONe)10 has been observed and an assignment based on the calculations in proposed.

First-principles study on the structure and electronic property of gas molecules adsorption on Ge2Li2 monolayer

NASA Astrophysics Data System (ADS)

Hu, Yiwei; Long, Linbo; Mao, Yuliang; Zhong, Jianxin

2018-06-01

Using first-principles methods, we have studied the adsorption of gas molecules (CO2, CH4, H2S, H2 and NH3) on two dimensional Ge2Li2 monolayer. The adsorption geometries, adsorption energies, charge transfer, and band structures of above mentioned gas molecules adsorption on Ge2Li2 monolayer are analyzed. It is found that the adsorption of CO2 on Ge2Li2 monolayer is a kind of strong chemisorption, while other gas molecules such as CH4, H2S, H2 and NH3 are physisorption. The strong covalent binding is formed between the CO2 molecule and the nearest Ge atom in Ge2Li2 monolayer. This adsorption of CO2 molecule on Ge2Li2 monolayer leads to a direct energy gap of 0.304 eV. Other gas molecules exhibit mainly ionic binding to the nearest Li atoms in Ge2Li2 monolayer, which leads to indirect energy gap after adsorptions. Furthermore, it is found that the work function of Ge2Li2 monolayer is sensitive with the variation of adsorbents. Our results reveal that the Ge2Li2 monolayer can be used as a kind of nano device for gas molecules sensor.

Use of small gap anastomosis for the repair of peripheral nerve injury by cutting and sleeve jointing the epineurium.

PubMed

Wang, Peiji; Zhao, Jiaju; Jiang, Bo; Zhang, Yong

2015-05-01

Although epineurium neurorrhaphy is the most reliable and conventional method for the repair of peripheral nerve injury and is accepted as the gold standard, it is still far from ideal. Many attempts have been made to develop nerve anastomosis techniques. The aim of this study was to investigate the use of small gap anastomosis performed by cutting and sleeve jointing the epineurium for nerve repair. A 12-week study was performed using small gap anastomosis via cutting and sleeve jointing the epineurium, compared with epineurium neurorrhaphy in situ, to repair a rat sciatic nerve rupture. Three experimental groups were included: sham control (n = 8), small gap anastomosis (n = 16), and epineurium neurorrhaphy (n = 16). About 12 weeks after surgery, recovery was assessed with walking track analysis, electrophysiology, hematoxylin and eosin staining, immunohistochemistry, and electron microscopy. The sciatic nerve functional index observed in the small gap anastomosis group was significantly higher than that in the epineurium neurorrhaphy group (p < 0.05). In vivo electrophysiological analysis confirmed that the small gap anastomosis group showed a significantly higher conduction velocity than the epineurium neurorrhaphy group (p < 0.05). Postoperative morphometric analysis revealed better results after small gap anastomosis compared with epineurium neurorrhaphy. Small gap anastomosis via cutting and sleeve jointing the epineurium could be an alternative to epineurium neurorrhaphy for the repair of peripheral nerve injury, particularly, considering that the epineurium originates from native tissue that provides a suitable microenvironment for the selective regeneration of axons. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Small molecule chemical probes of microRNA function.

PubMed

Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R; Disney, Matthew D

2015-02-01

MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as progress is made in understanding small molecule recognition of RNA. Copyright © 2014. Published by Elsevier Ltd.

3D nanostar dimers with a sub-10-nm gap for single-/few-molecule surface-enhanced raman scattering.

PubMed

Chirumamilla, Manohar; Toma, Andrea; Gopalakrishnan, Anisha; Das, Gobind; Zaccaria, Remo Proietti; Krahne, Roman; Rondanina, Eliana; Leoncini, Marco; Liberale, Carlo; De Angelis, Francesco; Di Fabrizio, Enzo

2014-04-16

Plasmonic nanostar-dimers, decoupled from the substrate, have been fabricated by combining electron-beam lithography and reactive-ion etching techniques. The 3D architecture, the sharp tips of the nanostars and the sub-10 nm gap size promote the formation of giant electric-field in highly localized hot-spots. The single/few molecule detection capability of the 3D nanostar-dimers has been demonstrated by Surface-Enhanced Raman Scattering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA.

PubMed

Velagapudi, Sai Pradeep; Luo, Yiling; Tran, Tuan; Haniff, Hafeez S; Nakai, Yoshio; Fallahi, Mohammad; Martinez, Gustavo J; Childs-Disney, Jessica L; Disney, Matthew D

2017-03-22

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.

Flow formed by spanwise gaps between roughness elements

NASA Technical Reports Server (NTRS)

Logan, E.; Lin, S. H.; Islam, O.

1985-01-01

Measurements of the three mean velocity components and the three Reynolds shear stresses were made in the region downstream of gaps between wall-mounted roughness elements of square cross section and high aspect ratio in a thick turbulent boundary layer. The effect of small and large gaps was studied in a wind tunnel at a Reynolds number of 3600, based on obstacle height and free-stream velocity. The small gap produces retardation of the gap flow as with a two-dimensional roughness element, but a definite interaction between gap and wake flows is observed. The interaction is more intense for the large gap than for the small. Both gaps generate a secondary crossflow which moves fluid away from the centerline in the wall region and toward the centerline in the outer (y greater than 1.5H) region.

Fabricating Atom-Sized Gaps by Field-Aided Atom Migration in Nanoscale Junctions

NASA Astrophysics Data System (ADS)

Liu, Ran; Bi, Jun-Jie; Xie, Zhen; Yin, Kaikai; Wang, Dunyou; Zhang, Guang-Ping; Xiang, Dong; Wang, Chuan-Kui; Li, Zong-Liang

2018-05-01

The gap sizes between electrodes generated by typical methods are generally much larger than the dimension of a common molecule when fabricating a single-molecule junction, which dramatically suppresses the yield of single-molecule junctions. Based on the ab initio calculations, we develop a strategy named the field-aided method to accurately fabricate an atomic-sized gap between gold nanoelectrodes. To understand the mechanism of this strategy, configuration evolutions of gold nanojunction in stretching and compressing processes are calculated. The numerical results show that, in the stretching process, the gold atoms bridged between two electrodes are likely to form atomic chains. More significantly, lattice vacant positions can be easily generated in stretching and compressing processes, which make field-aided gap generation possible. In field-aided atom migration (FAAM), the external field can exert driving force, enhance the initial energy of the system, and decrease the barrier in the migration path, which makes the atom migration feasible. Conductance and stretching and compressing forces, as measurable variables in stretching and compressing processes, present very useful signals for determining the time to perform FAAM. Following this desirable strategy, we successfully fabricate gold nanogaps with a dimension of 0.38 ±0.05 nm in the experiment, as our calculation simulates.

[Effects of forest gap size and light intensity on herbaceous plants in Pinus koraiensis-dominated broadleaved mixed forest].

PubMed

Duan, Wen-Biao; Wang, Li-Xia; Chen, Li-Xin; Du, Shan; Wei, Quan-Shuai; Zhao, Jian-Hui

2013-03-01

1 m x 1 m fixed quadrats were parallelly arranged with a space of 2 m in each of six forest gaps in Pinus koraiensis-dominated broadleaved mixed forest, taking the gap center as the starting point and along east-west and south-north directions. In each quadrat, the coverage and abundance of herbaceous plants at different height levels were investigated by estimation method in June and September 2011, and the matrix characteristics within the quadrats were recorded. Canopy analyzer was used to take fish-eye photos in the selected overcast days in each month from June to September, 2011, and the relative light intensity was calculated by using Gap Light Analyzer 2.0 software. The differences in the relative light intensity and herbaceous plants coverage and richness between different gaps as well as the correlations between the coverage of each species and the direct light, diffuse light, and matrix were analyzed. The results showed that in opening areas and under canopy, the relative light intensity in large gaps was higher than that in small gaps, and the variation ranges of diffuse light and direct light from gap center to gap edge were bigger in large gaps than in small gaps. The direct light reaching at the ground both in large gaps and in small gaps was higher in the north than in the south direction. In the Z1, Z2, Z3, and Z4 zones, both the coverage and the richness of herbaceous plants were larger in large gaps than in small gaps, and the differences of species richness between large and small gaps reached significant level. The coverage of the majority of the herbaceous plants had significant correlations with diffuse light and matrix, and only the coverage of a few herbaceous plants was correlated with direct light.

Small Molecule Inhibitors of AI-2 Signaling in Bacteria: State-of-the-Art and Future Perspectives for Anti-Quorum Sensing Agents

PubMed Central

Guo, Min; Gamby, Sonja; Zheng, Yue; Sintim, Herman O.

2013-01-01

Bacteria respond to different small molecules that are produced by other neighboring bacteria. These molecules, called autoinducers, are classified as intraspecies (i.e., molecules produced and perceived by the same bacterial species) or interspecies (molecules that are produced and sensed between different bacterial species). AI-2 has been proposed as an interspecies autoinducer and has been shown to regulate different bacterial physiology as well as affect virulence factor production and biofilm formation in some bacteria, including bacteria of clinical relevance. Several groups have embarked on the development of small molecules that could be used to perturb AI-2 signaling in bacteria, with the ultimate goal that these molecules could be used to inhibit bacterial virulence and biofilm formation. Additionally, these molecules have the potential to be used in synthetic biology applications whereby these small molecules are used as inputs to switch on and off AI-2 receptors. In this review, we highlight the state-of-the-art in the development of small molecules that perturb AI-2 signaling in bacteria and offer our perspective on the future development and applications of these classes of molecules. PMID:23994835

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria.

PubMed

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-22

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria

NASA Astrophysics Data System (ADS)

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-01

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

[Effects of forest gap size and uprooted microsite on the microclimate in Pinus koraiensis-dominated broad-leaved mixed forest].

PubMed

Duan, Wen-biao; Du, Shan; Chen, Li-xin; Wang, Li-xia; Wei, Quan-shuai; Zhao, Jian-hui

2013-08-01

Three representative forest gaps with pit-mound microsites formed by uprooted trees were selected within the 2.55 hm2 plot in a Pinus koraiensis-dominated broad-leaved mixed forest in Xiao Xing'an Mountains of Northeast China. The cleared land and closed stand were set up as the controls, and the PAR, air temperature and relative humidity in the centers of different size gaps and in mound top as well as the total radiation and precipitation in the gap centers were measured between July and September, 2011 by using multichannel automatic meteorological stations. The differences of the microclimate between the gap centers and mound top in different months were compared, and the monthly and diurnal variations of the microclimatic factors in the gap centers and in the mound top under typical weather conditions were analyzed. The results showed that the mean monthly PAR and air temperature in the three gaps of different sizes were in the order of large gap > medium gap > small gap, and the mean monthly relative humidity was in the order of small gap > medium gap > large gap. For the same size gap, the mean monthly PAR and air temperature were higher in the mound top than in the gap center, whereas the mean monthly relative humidity was higher in the gap center than in the mound top. Both the mean monthly total radiation and the mean monthly air temperature in the forest gaps and in the controls were in the order of July > August > September and of cleared land > large gap > medium gap > small gap > closed stand, while the mean monthly relative humidity was in the order of closed stand > small gap > medium gap > large gap > cleared land. The differences in the mean monthly relative humidity between closed stand and various gaps and between closed stand and cleared land reached significant level. The monthly precipitation from July to September decreased in the order of cleared land > large gap > medium gap > small gap > closed stand. Whether in sunny days or in overcast days, the mean daily PAR and air temperature were higher in mound top than in gap center, and the mean daily relative humidity was in opposite. Whether in mound top or in gap center, the mean daily PAR and air temperature were higher in sunny days than in overcast days, while the mean daily relative humidity was higher in overcast days than in sunny days.

DFT/TD-DFT study on the electronic and spectroscopic properties of hollow cubic and hollow spherical (ZnO) m quantum dots interacting with CO, NO2 and SO3 molecules

NASA Astrophysics Data System (ADS)

Gopalakrishnan, Sankarasubramanian; Shankar, Ramasamy; Kolandaivel, Ponmalai

2018-03-01

Hollow spherical (HS) and hollow cubic (HC) (ZnO) m quantum dots (QDs) were constructed and optimized using density functional theory (DFT) method. CO, NO2 and SO3 molecules were used to interact with the HC and HS (ZnO) m QDs at the centre and on the surface of the QDs. The changes in the electronic energy levels of HC and HS (ZnO) m QDs due to the interactions of CO, NO2 and SO3 molecules have been studied. The electronic and spectroscopic properties, such as density of states, HOMO-LUMO energy gap, absorption spectra, IR and Raman spectra of HC and HS (ZnO) m QDs have been studied using DFT and Time dependent-DFT (TD-DFT) methods. The interaction energy values show that the SO3 molecule has strongly interacted with HC and HS (ZnO) m QDs than the CO and NO2 molecules. The results of the density of states show that the HC QDs have peaks that are very close to each other, whereas the same is found to be broad in the HS QDs. The HOMO-LUMO energy gap is more for the HS QDs than the HC QDs, and also it gets decreased, when the NO2 and SO3 molecules interact at the centre of the HC and HS (ZnO) m QDs. The blue and red shifts were observed in the absorption spectra of HS and HC QDs. The natural transition orbital (NTO) plot reveals that the interaction of the molecules on the surface of the QDs reduce the chance of electron-hole recombination; hence the energy gap increases for NO2 and SO3 molecular interactions on the surface of the HC and HS (ZnO) m QDs. The vibrational assignments have been made for HC and HS QDs interacting with CO, NO2 and SO3 molecules.

Organic small molecule semiconducting chromophores for use in organic electronic devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Welch, Gregory C.; Hoven, Corey V.; Nguyen, Thuc-Quyen

Small organic molecule semi-conducting chromophores containing a pyridalthiadiazole, pyridaloxadiazole, or pyridaltriazole core structure are disclosed. Such compounds can be used in organic heterojunction devices, such as organic small molecule solar cells and transistors.

Structure-guided Discovery of Dual-recognition Chemibodies.

PubMed

Cheng, Alan C; Doherty, Elizabeth M; Johnstone, Sheree; DiMauro, Erin F; Dao, Jennifer; Luthra, Abhinav; Ye, Jay; Tang, Jie; Nixey, Thomas; Min, Xiaoshan; Tagari, Philip; Miranda, Les P; Wang, Zhulun

2018-05-15

Small molecules and antibodies each have advantages and limitations as therapeutics. Here, we present for the first time to our knowledge, the structure-guided design of "chemibodies" as small molecule-antibody hybrids that offer dual recognition of a single target by both a small molecule and an antibody, using DPP-IV enzyme as a proof of concept study. Biochemical characterization demonstrates that the chemibodies present superior DPP-IV inhibition compared to either small molecule or antibody component alone. We validated our design by successfully solving a co-crystal structure of a chemibody in complex with DPP-IV, confirming specific binding of the small molecule portion at the interior catalytic site and the Fab portion at the protein surface. The discovery of chemibodies presents considerable potential for novel therapeutics that harness the power of both small molecule and antibody modalities to achieve superior specificity, potency, and pharmacokinetic properties.

Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts.

PubMed

Disney, Matthew D

2013-12-01

RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

Advancing Biological Understanding and Therapeutics Discovery with Small Molecule Probes

PubMed Central

Schreiber, Stuart L.; Kotz, Joanne D.; Li, Min; Aubé, Jeffrey; Austin, Christopher P.; Reed, John C.; Rosen, Hugh; White, E. Lucile; Sklar, Larry A.; Lindsley, Craig W.; Alexander, Benjamin R.; Bittker, Joshua A.; Clemons, Paul A.; de Souza, Andrea; Foley, Michael A.; Palmer, Michelle; Shamji, Alykhan F.; Wawer, Mathias J.; McManus, Owen; Wu, Meng; Zou, Beiyan; Yu, Haibo; Golden, Jennifer E.; Schoenen, Frank J.; Simeonov, Anton; Jadhav, Ajit; Jackson, Michael R.; Pinkerton, Anthony B.; Chung, Thomas D.Y.; Griffin, Patrick R.; Cravatt, Benjamin F.; Hodder, Peter S.; Roush, William R.; Roberts, Edward; Chung, Dong-Hoon; Jonsson, Colleen B.; Noah, James W.; Severson, William E.; Ananthan, Subramaniam; Edwards, Bruce; Oprea, Tudor I.; Conn, P. Jeffrey; Hopkins, Corey R.; Wood, Michael R.; Stauffer, Shaun R.; Emmitte, Kyle A.

2015-01-01

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery. PMID:26046436

High mobility high efficiency organic films based on pure organic materials

DOEpatents

Salzman, Rhonda F [Ann Arbor, MI; Forrest, Stephen R [Ann Arbor, MI

2009-01-27

A method of purifying small molecule organic material, performed as a series of operations beginning with a first sample of the organic small molecule material. The first step is to purify the organic small molecule material by thermal gradient sublimation. The second step is to test the purity of at least one sample from the purified organic small molecule material by spectroscopy. The third step is to repeat the first through third steps on the purified small molecule material if the spectroscopic testing reveals any peaks exceeding a threshold percentage of a magnitude of a characteristic peak of a target organic small molecule. The steps are performed at least twice. The threshold percentage is at most 10%. Preferably the threshold percentage is 5% and more preferably 2%. The threshold percentage may be selected based on the spectra of past samples that achieved target performance characteristics in finished devices.

Characterizing protein domain associations by Small-molecule ligand binding

PubMed Central

Li, Qingliang; Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

2012-01-01

Background Protein domains are evolutionarily conserved building blocks for protein structure and function, which are conventionally identified based on protein sequence or structure similarity. Small molecule binding domains are of great importance for the recognition of small molecules in biological systems and drug development. Many small molecules, including drugs, have been increasingly identified to bind to multiple targets, leading to promiscuous interactions with protein domains. Thus, a large scale characterization of the protein domains and their associations with respect to small-molecule binding is of particular interest to system biology research, drug target identification, as well as drug repurposing. Methods We compiled a collection of 13,822 physical interactions of small molecules and protein domains derived from the Protein Data Bank (PDB) structures. Based on the chemical similarity of these small molecules, we characterized pairwise associations of the protein domains and further investigated their global associations from a network point of view. Results We found that protein domains, despite lack of similarity in sequence and structure, were comprehensively associated through binding the same or similar small-molecule ligands. Moreover, we identified modules in the domain network that consisted of closely related protein domains by sharing similar biochemical mechanisms, being involved in relevant biological pathways, or being regulated by the same cognate cofactors. Conclusions A novel protein domain relationship was identified in the context of small-molecule binding, which is complementary to those identified by traditional sequence-based or structure-based approaches. The protein domain network constructed in the present study provides a novel perspective for chemogenomic study and network pharmacology, as well as target identification for drug repurposing. PMID:23745168

Proteoform-specific protein binding of small molecules in complex matrices

USDA-ARS?s Scientific Manuscript database

Characterizing the specific binding between protein targets and small molecules is critically important for drug discovery. Conventional assays require isolation and purification of small molecules from complex matrices through multistep chromatographic fractionation, which may alter their original ...

DNA Origami Directed Au Nanostar Dimers for Single-Molecule Surface-Enhanced Raman Scattering.

PubMed

Tanwar, Swati; Haldar, Krishna Kanta; Sen, Tapasi

2017-12-06

We demonstrate the synthesis of Au nanostar dimers with tunable interparticle gap and controlled stoichiometry assembled on DNA origami. Au nanostars with uniform and sharp tips were immobilized on rectangular DNA origami dimerized structures to create nanoantennas containing monomeric and dimeric Au nanostars. Single Texas red (TR) dye was specifically attached in the junction of the dimerized origami to act as a Raman reporter molecule. The SERS enhancement factors of single TR dye molecules located in the conjunction region in dimer structures having interparticle gaps of 7 and 13 nm are 2 × 10 10 and 8 × 10 9 , respectively, which are strong enough for single analyte detection. The highly enhanced electromagnetic field generated by the plasmon coupling between sharp tips and cores of two Au nanostars in the wide conjunction region allows the accommodation and specific detection of large biomolecules. Such DNA-directed assembled nanoantennas with controlled interparticle separation distance and stoichiometry, and well-defined geometry, can be used as excellent substrates in single-molecule SERS spectroscopy and will have potential applications as a reproducible platform in single-molecule sensing.

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling

PubMed Central

Wagner, Bridget K.; Clemons, Paul A.

2009-01-01

Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene-expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe- and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of “virtual” profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe and drug discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections. PMID:19825513

Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction.

PubMed

Song, Yunke; Zhang, Yi; Wang, Tza-Huei

2013-04-08

Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small Molecule based Musculoskeletal Regenerative Engineering

PubMed Central

Lo, Kevin W.-H.; Jiang, Tao; Gagnon, Keith A.; Nelson, Clarke; Laurencin, Cato T.

2014-01-01

Clinicians and scientists working in the field of regenerative engineering are actively investigating a wide range of methods to promote musculoskeletal tissue regeneration. Small molecule-mediated tissue regeneration is emerging as a promising strategy for regenerating various musculoskeletal tissues and a large number of small molecule compounds have been recently discovered as potential bioactive molecules for musculoskeletal tissue repair and regeneration. In this review, we summarize the recent literature encompassing the past four years in the area of small bioactive molecule for promoting repair and regeneration of various musculoskeletal tissues including bone, muscle, cartilage, tendon, and nerve. PMID:24405851

Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

PubMed Central

2017-01-01

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif–small molecule interactions identified via selection. Named High Throughput Structure–Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif–small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule–RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs. PMID:28386598

ArhGAP15, a Rac-specific GTPase-activating Protein, Plays a Dual Role in Inhibiting Small GTPase Signaling*

PubMed Central

Radu, Maria; Rawat, Sonali J.; Beeser, Alexander; Iliuk, Anton; Tao, Weiguo Andy; Chernoff, Jonathan

2013-01-01

Signaling from small GTPases is a tightly regulated process. In this work we used a protein microarray screen to identify the Rac-specific GAP, ArhGAP15, as a substrate of the Rac effectors Pak1 and Pak2. In addition to serving as a substrate of Pak1/2, we found that ArhGAP15, via its PH domain, bound to these kinases. The association of ArhGAP15 to Pak1/2 resulted in mutual inhibition of GAP and kinase catalytic activity, respectively. Knock-down of ArhGAP15 resulted in activation of Pak1/2, both indirectly, as a result of Rac activation, and directly, as a result of disruption of the ArhGAP15/Pak complex. Our data suggest that ArhGAP15 plays a dual negative role in regulating small GTPase signaling, by acting at the level of the GTPase itself, as well interacting with its effector, Pak kinase. PMID:23760270

Understanding the Halogenation Effects in Diketopyrrolopyrrole-Based Small Molecule Photovoltaics.

PubMed

Sun, Shi-Xin; Huo, Yong; Li, Miao-Miao; Hu, Xiaowen; Zhang, Hai-Jun; Zhang, You-Wen; Zhang, You-Dan; Chen, Xiao-Long; Shi, Zi-Fa; Gong, Xiong; Chen, Yongsheng; Zhang, Hao-Li

2015-09-16

Two molecules containing a central diketopyrrolopyrrole and two oligothiophene units have been designed and synthesized. Comparisons between the molecules containing terminal F (FDPP) and Cl (CDPP) atoms allowed us to evaluate the effects of halogenation on the photovoltaic properties of the small molecule organic solar cells (OSCs). The OSCs devices employing FDPP:PC71BM films showed power conversion efficiencies up to 4.32%, suggesting that fluorination is an efficient method for constructing small molecules for OSCs.

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

NASA Astrophysics Data System (ADS)

Kortagere, Sandhya; Welsh, William J.

2006-12-01

G-protein coupled receptors (GPCRs) comprise a large superfamily of proteins that are targets for nearly 50% of drugs in clinical use today. In the past, the use of structure-based drug design strategies to develop better drug candidates has been severely hampered due to the absence of the receptor's three-dimensional structure. However, with recent advances in molecular modeling techniques and better computing power, atomic level details of these receptors can be derived from computationally derived molecular models. Using information from these models coupled with experimental evidence, it has become feasible to build receptor pharmacophores. In this study, we demonstrate the use of the Hybrid Structure Based (HSB) method that can be used effectively to screen and identify prospective ligands that bind to GPCRs. Essentially; this multi-step method combines ligand-based methods for building enriched libraries of small molecules and structure-based methods for screening molecules against the GPCR target. The HSB method was validated to identify retinal and its analogues from a random dataset of ˜300,000 molecules. The results from this study showed that the 9 top-ranking molecules are indeed analogues of retinal. The method was also tested to identify analogues of dopamine binding to the dopamine D2 receptor. Six of the ten top-ranking molecules are known analogues of dopamine including a prodrug, while the other thirty-four molecules are currently being tested for their activity against all dopamine receptors. The results from both these test cases have proved that the HSB method provides a realistic solution to bridge the gap between the ever-increasing demand for new drugs to treat psychiatric disorders and the lack of efficient screening methods for GPCRs.

Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital-configuration interaction based quantum master equation study

NASA Astrophysics Data System (ADS)

Kishi, Ryohei; Minami, Takuya; Fukui, Hitoshi; Takahashi, Hideaki; Nakano, Masayoshi

2008-06-01

The core molecule dependence of energy (exciton) migration in phenylacetylene nanostar dendrimers is investigated using the ab initio molecular orbital (MO)-configuration interaction based quantum master equation approach. We examine three kinds of core molecular species, i.e., benzene, anthracene, and pentacene, with different highest occupied MO-lowest unoccupied MO (HOMO-LUMO) gaps, which lead to different orbital interactions between the dendron parts and the core molecule. The nanostars bearing anthracene and pentacene cores are characterized by multistep exciton states with spatially well-segmented distributions: The exciton distributions of high-lying exciton states are spatially localized well in the periphery region, whereas those of low-lying exciton states are done in the core region. On the other hand, for the nanostar bearing benzene core, which also has multistep exciton states, the spatial exciton distributions of low-lying exciton states are delocalized over the dendron and the core regions. It is found that the former nanostars exhibit nearly complete exciton migration from the periphery to the core molecule in contrast to the latter one, in which significant exciton distribution remains in the dendron parts attached to the core after the exciton relaxation, although all these dendrimers exhibit fast exciton relaxation from the initially populated states. It is predicted from the analysis based on the MO correlation diagrams and the relative relaxation factor that the complete exciton migration to the core occurs not only when the HOMO-LUMO gap of the core molecule is nearly equal to that of the dendron parts attached to the core (anthracene case) but also when fairly smaller than that (pentacene case), whereas the complete migration is not achieved when the HOMO-LUMO gap of the core is larger than that of the dendron parts (benzene case). These results suggest that the fast and complete exciton migration of real dendrimers could be realized by adjusting the HOMO-LUMO gap of the core molecule to be smaller than that of dendron parts, although there exist more complicated relaxation processes as compared to simple dendritic aggregate models studied so far.

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset | Office of Cancer Genomics

Cancer.gov

Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer medicines. Cancer cell-line (CCL) profiling of small-molecule sensitivity has emerged as an unbiased method to assess the relationships between genetic or cellular features of CCLs and small-molecule response. Here, we developed annotated cluster multidimensional enrichment analysis to explore the associations between groups of small molecules and groups of CCLs in a new, quantitative sensitivity dataset.

A Nonfullerene Small Molecule Acceptor with 3D Interlocking Geometry Enabling Efficient Organic Solar Cells.

PubMed

Lee, Jaewon; Singh, Ranbir; Sin, Dong Hun; Kim, Heung Gyu; Song, Kyu Chan; Cho, Kilwon

2016-01-06

A new 3D nonfullerene small-molecule acceptor is reported. The 3D interlocking geometry of the small-molecule acceptor enables uniform molecular conformation and strong intermolecular connectivity, facilitating favorable nanoscale phase separation and electron charge transfer. By employing both a novel polymer donor and a nonfullerene small-molecule acceptor in the solution-processed organic solar cells, a high-power conversion efficiency of close to 6% is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A "roller-wheel" Pt-containing small molecule that outperforms its polymer analogs in organic solar cells

DOE PAGES

He, Wenhan; Wu, Qin; Livshits, Maksim Y.; ...

2016-05-23

A novel Pt-bisacetylide small molecule (Pt-SM) featuring “roller-wheel” geometry was synthesized and characterized. When compared with conventional Pt-containing polymers and small molecules having “dumbbell” shaped structures, Pt-SM displays enhanced crystallinity and intermolecular π–π interactions, as well as favorable panchromatic absorption behaviors. Furthermore, organic solar cells (OSCs) employing Pt-SM achieve power conversion efficiencies (PCEs) up to 5.9%, the highest reported so far for Pt-containing polymers and small molecules.

A "roller-wheel" Pt-containing small molecule that outperforms its polymer analogs in organic solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Wenhan; Wu, Qin; Livshits, Maksim Y.

A novel Pt-bisacetylide small molecule (Pt-SM) featuring “roller-wheel” geometry was synthesized and characterized. When compared with conventional Pt-containing polymers and small molecules having “dumbbell” shaped structures, Pt-SM displays enhanced crystallinity and intermolecular π–π interactions, as well as favorable panchromatic absorption behaviors. Furthermore, organic solar cells (OSCs) employing Pt-SM achieve power conversion efficiencies (PCEs) up to 5.9%, the highest reported so far for Pt-containing polymers and small molecules.

Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage.

PubMed

Lobo, Elena; Dalling, James W

2014-03-07

Treefall gaps play an important role in tropical forest dynamics and in determining above-ground biomass (AGB). However, our understanding of gap disturbance regimes is largely based either on surveys of forest plots that are small relative to spatial variation in gap disturbance, or on satellite imagery, which cannot accurately detect small gaps. We used high-resolution light detection and ranging data from a 1500 ha forest in Panama to: (i) determine how gap disturbance parameters are influenced by study area size, and the criteria used to define gaps; and (ii) to evaluate how accurately previous ground-based canopy height sampling can determine the size and location of gaps. We found that plot-scale disturbance parameters frequently differed significantly from those measured at the landscape-level, and that canopy height thresholds used to define gaps strongly influenced the gap-size distribution, an important metric influencing AGB. Furthermore, simulated ground surveys of canopy height frequently misrepresented the true location of gaps, which may affect conclusions about how relatively small canopy gaps affect successional processes and contribute to the maintenance of diversity. Across site comparisons need to consider how gap definition, scale and spatial resolution affect characterizations of gap disturbance, and its inferred importance for carbon storage and community composition.

A-π-D-π-A Electron-Donating Small Molecules for Solution-Processed Organic Solar Cells: A Review.

PubMed

Wang, Zhen; Zhu, Lingyun; Shuai, Zhigang; Wei, Zhixiang

2017-11-01

Organic solar cells based on semiconducting polymers and small molecules have attracted considerable attention in the last two decades. Moreover, the power conversion efficiencies for solution-processed solar cells containing A-π-D-π-A-type small molecules and fullerenes have reached 11%. However, the method for designing high-performance, photovoltaic small molecules still remains unclear. In this review, recent studies on A-π-D-π-A electron-donating small molecules for organic solar cells are introduced. Moreover, the relationships between molecular properties and device performances are summarized, from which inspiration for the future design of high performance organic solar cells may be obtained. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A general electrochemical method for label-free screening of protein–small molecule interactions†

PubMed Central

Cash, Kevin J.; Ricci, Francesco

2010-01-01

Here we report a versatile method by which the interaction between a protein and a small molecule, and the disruption of that interaction by competition with other small molecules, can be monitored electrochemically directly in complex sample matrices. PMID:19826675

Toward Generalization of Iterative Small Molecule Synthesis

PubMed Central

Lehmann, Jonathan W.; Blair, Daniel J.; Burke, Martin D.

2018-01-01

Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the “building block approach”, i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach. PMID:29696152

Bridging the Gap Between Stationary Homogeneous Isotropic Turbulence and Quantum Mechanics

NASA Astrophysics Data System (ADS)

Sohrab, Siavash

A statistical theory of stationary isotropic turbulence is presented with eddies possessing Gaussian velocity distribution, Maxwell-Boltzmann speed distribution in harmony with perceptions of Heisenberg, and Planck energy distribution in harmony with perceptions of Chandrasekhar and in agreement with experimental observations of Van Atta and Chen. Defining the action S = - mΦ in terms of velocity potential of atomic motion, scale-invariant Schrödinger equation is derivedfrom invariant Bernoulli equation. Thus, the gap between the problems of turbulence and quantum mechanics is closed through connections between Cauchy-Euler-Bernoulli equations of hydrodynamics, Hamilton-Jacobi equation of classical mechanics, and finally Schrödinger equation of quantum mechanics. Transitions of particle (molecular cluster cji) from a small rapidly-oscillating eddy ej (high-energy level-j) to a large slowly-oscillating eddy ei (low energy-level-i) leads to emission of a sub-particle (molecule mji) that carries away the excess energy ɛji = h (νj -νi) in harmony with Bohr theory of atomic spectra. ∖ ∖ NASA Grant No. NAG3-1863.

An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure.

PubMed

Bhagavat, Raghu; Sankar, Santhosh; Srinivasan, Narayanaswamy; Chandra, Nagasuma

2018-03-06

Protein-ligand interactions form the basis of most cellular events. Identifying ligand binding pockets in proteins will greatly facilitate rationalizing and predicting protein function. Ligand binding sites are unknown for many proteins of known three-dimensional (3D) structure, creating a gap in our understanding of protein structure-function relationships. To bridge this gap, we detect pockets in proteins of known 3D structures, using computational techniques. This augmented pocketome (PocketDB) consists of 249,096 pockets, which is about seven times larger than what is currently known. We deduce possible ligand associations for about 46% of the newly identified pockets. The augmented pocketome, when subjected to clustering based on similarities among pockets, yielded 2,161 site types, which are associated with 1,037 ligand types, together providing fold-site-type-ligand-type associations. The PocketDB resource facilitates a structure-based function annotation, delineation of the structural basis of ligand recognition, and provides functional clues for domains of unknown functions, allosteric proteins, and druggable pockets. Copyright © 2018 Elsevier Ltd. All rights reserved.

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

PubMed

Lee, Hui Sun; Im, Wonpil

2017-01-01

Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

How does the plasmonic enhancement of molecular absorption depend on the energy gap between molecular excitation and plasmon modes: a mixed TDDFT/FDTD investigation.

PubMed

Sun, Jin; Li, Guang; Liang, WanZhen

2015-07-14

A real-time time-dependent density functional theory coupled with the classical electrodynamics finite difference time domain technique is employed to systematically investigate the optical properties of hybrid systems composed of silver nanoparticles (NPs) and organic adsorbates. The results demonstrate that the molecular absorption spectra throughout the whole energy range can be enhanced by the surface plasmon resonance of Ag NPs; however, the absorption enhancement ratio (AER) for each absorption band differs significantly from the others, leading to the quite different spectral profiles of the hybrid complexes in contrast to those of isolated molecules or sole NPs. Detailed investigations reveal that the AER is sensitive to the energy gap between the molecular excitation and plasmon modes. As anticipated, two separate absorption bands, corresponding to the isolated molecules and sole NPs, have been observed at a large energy gap. When the energy gap approaches zero, the molecular excitation strongly couples with the plasmon mode to form the hybrid exciton band, which possesses the significantly enhanced absorption intensity, a red-shifted peak position, a surprising strongly asymmetric shape of the absorption band, and the nonlinear Fano effect. Furthermore, the dependence of surface localized fields and the scattering response functions (SRFs) on the geometrical parameters of NPs, the NP-molecule separation distance, and the external-field polarizations has also been depicted.

Study on Gap Flow Field Simulation in Small Hole Machining of Ultrasonic Assisted EDM

NASA Astrophysics Data System (ADS)

Liu, Yu; Chang, Hao; Zhang, Wenchao; Ma, Fujian; Sha, Zhihua; Zhang, Shengfang

2017-12-01

When machining a small hole with high aspect ratio in EDM, it is hard for the flushing liquid entering the bottom gap and the debris could hardly be removed, which results in the accumulation of debris and affects the machining efficiency and machining accuracy. The assisted ultrasonic vibration can improve the removal of debris in the gap. Based on dynamics simulation software Fluent, a 3D model of debris movement in the gap flow field of EDM small hole machining assisted with side flushing and ultrasonic vibration is established in this paper. When depth to ratio is 3, the laws of different amplitudes and frequencies on debris distribution and removal are quantitatively analysed. The research results show that periodic ultrasonic vibration can promote the movement of debris, which is beneficial to the removal of debris in the machining gap. Compared to traditional small hole machining in EDM, the debris in the machining gap is greatly reduced, which ensures the stability of machining process and improves the machining efficiency.

Raising awareness of the importance of funding for tuberculosis small-molecule research.

PubMed

Riccardi, Giovanna; Old, Iain G; Ekins, Sean

2017-03-01

Tuberculosis (TB) drug discovery research is hampered by several factors, but as in many research areas, the available funding is insufficient to support the needs of research and development. Recent years have seen various large collaborative efforts involving public-private partnerships, mimicking the situation during the golden age of antibiotic drug discovery during the 1950s and 1960s. The large-scale collaborative efforts funded by the European Union (EU) are now subject to diminishing financial support. As a result, TB researchers are increasingly looking for novel forms of funding, such as crowdfunding, to fill this gap. Any potential solution will require a careful reassessment of the incentives to encourage additional organizations to provide funding. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bis(aminoaryl) Carbon-Bridged Oligo(phenylenevinylene)s Expand the Limits of Electronic Couplings.

PubMed

Burrezo, Paula Mayorga; Lin, Nai-Ti; Nakabayashi, Koji; Ohkoshi, Shin-Ichi; Calzado, Eva M; Boj, Pedro G; Díaz García, María A; Franco, Carlos; Rovira, Concepciò; Veciana, Jaume; Moos, Michael; Lambert, Christoph; López Navarrete, Juan T; Tsuji, Hayato; Nakamura, Eiichi; Casado, Juan

2017-03-06

Carbon-bridged bis(aminoaryl) oligo(para-phenylenevinylene)s have been prepared and their optical, electrochemical, and structural properties analyzed. Their radical cations are class III and class II mixed-valence systems, depending on the molecular size, and they show electronic couplings which are among the largest for the self-exchange reaction of purely organic molecules. In their dication states, the antiferromagnetic coupling is progressively tuned with size from quinoidal closed-shell to open-shell biradicals. The data prove that the electronic coupling in the radical cations and the singlet-triplet gap in the dications show similar small attenuation factors, thus allowing charge/spin transfer over rather large distances. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Screening of Small Molecule Interactor Library by Using In-Cell NMR Spectroscopy (SMILI-NMR)

PubMed Central

Xie, Jingjing; Thapa, Rajiv; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander

2011-01-01

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP–FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast. PMID:19422228

Multiscale investigation of chemical interference in proteins

NASA Astrophysics Data System (ADS)

Samiotakis, Antonios; Homouz, Dirar; Cheung, Margaret S.

2010-05-01

We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side-chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules. In this regard, MultiSCAAL is a promising and effective sampling scheme for investigating chemical interference which presents a great challenge when modeling protein interactions in vivo.

Interactions of quercetin, curcumin, epigallocatechin gallate and folic acid with gelatin.

PubMed

Yang, Tingting; Yang, Huiru; Fan, Yan; Li, Bafang; Hou, Hu

2018-06-15

Some small bioactive molecules from food show the potential health benefits, but with poor chemical stability and bioavailability. The interactions between small molecules and gelatin were investigated. Fluorescence experiments demonstrated that the bimolecular quenching constants (k q ) of complexes (gelatin-quercetin, gelatin-curcumin, gelatin-epigallocatechin gallate, gelatin-folic acid) were 3.7 × 10 12  L·mol -1 ·s -1 , 1.4 × 10 12  L·mol -1 ·s -1 , 2.7 × 10 12  L·mol -1 ·s -1 and 8.5 × 10 12  L·mol -1 ·s -1 , indicating that fluorescence quenching did not arise from a dynamical mechanism, but from gelatin-small molecules binding. Furthermore, the affinity with gelatin was ranked in the order of folic acid > quercetin > epigallocatechin gallate > curcumin. Fluorescence spectroscopy, ultraviolet and visible absorption spectroscopy, FTIR and circular dichroism showed that the interactions between small molecules and gelatin did not significantly alter the conformation and secondary structure of gelatin. Non-covalent interactions may result in the binding of gelatin with small molecules. The interactions were considered to be through two modes: (1) small molecules bound within the hydrophobic pockets of gelatin; (2) small molecules surrounded the gelatin molecule mainly through hydrogen bonds and hydrophobic interactions. Copyright © 2018 Elsevier B.V. All rights reserved.

Direct antigen presentation and gap junction mediated cross-presentation during apoptosis.

PubMed

Pang, Baoxu; Neijssen, Joost; Qiao, Xiaohang; Janssen, Lennert; Janssen, Hans; Lippuner, Christoph; Neefjes, Jacques

2009-07-15

MHC class I molecules present peptides from endogenous proteins. Ags can also be presented when derived from extracellular sources in the form of apoptotic bodies. Cross-presentation of such Ags by dendritic cells is required for proper CTL responses. The fate of Ags in cells initiated for apoptosis is unclear as is the mechanism of apoptosis-derived Ag transfer into dendritic cells. Here we show that novel Ags can be generated by caspases and be presented by MHC class I molecules of apoptotic cells. Since gap junctions function until apoptotic cells remodel to form apoptotic bodies, transfer and cross-presentation of apoptotic peptides by neighboring and dendritic cells occurs. We thus define a novel phase in classical Ag presentation and cross-presentation by MHC class I molecules: presentation of Ags created by caspase activities in cells in apoptosis.

Strong interaction between dye molecule and electromagnetic field localized around 1 Nm3 at gaps of nanoparticle dimers by plasmon resonance

NASA Astrophysics Data System (ADS)

Itoh, Tamitake; Yamamoto, Yuko S.

2017-11-01

Electronic transition rates of a molecule located at a crevasse or a gap of a plasmonic nanoparticle (NP) dimer are largely enhanced up to the factor of around 106 due to electromagnetic (EM) coupling between plasmonic and molecular electronic resonances. The coupling rate is determined by mode density of the EM fields at the crevasse and the oscillator strength of the local electronic resonance of a molecule. The enhancement by EM coupling at a gap of plasmonic NP dimer enables us single molecule (SM) Raman spectroscopy. Recently, this type of research has entered a new regime wherein EM enhancement effects cannot be treated by conventional theorems, namely EM mechanism. Thus, such theorems used for the EM enhancement effect should be re-examined. We here firstly summarize EM mechanism by using surface-enhanced Raman scattering (SERS), which is common in EM enhancement phenomena. Secondly, we focus on recent two our studies on probing SM fluctuation by SERS within the spatial resolution of sub-nanometer scales. Finally, we discuss the necessity of re-examining the EM mechanism with respect to two-fold breakdowns of the weak coupling assumption: the breakdown of Kasha's rule induced by the ultra-fast plasmonic de-excitation and the breakdown of the weak coupling by EM coupling rates exceeding both the plasmonic and molecular excitonic dephasing rates.

Pathogenic Cx31 is un/misfolded to cause skin abnormality via a Fos/JunB-mediated mechanism.

PubMed

Tang, Chengyuan; Chen, Xiang; Chi, Jingwei; Yang, Dawei; Liu, Shu; Liu, Mujun; Pan, Qian; Fan, Jianbing; Wang, Danling; Zhang, Zhuohua

2015-11-01

Mutations in connexin-31 (Cx31) are associated with multiple human diseases, including familial erythrokeratodermia variabilis (EKV). The pathogenic mechanism of EKV-associated Cx31 mutants remains largely elusive. Here, we show that EKV-pathogenic Cx31 mutants are un/misfolded and temperature sensitive. In Drosophila, expression of pathogenic Cx31, but not wild-type Cx31, causes depigmentation and degeneration of ommatidia that are rescued by expression of either dBip or dHsp70. Ectopic expression of Cx31 in mouse skin results in skin abnormalities resembling human EKV. The affected tissues show remarkable disrupted gap junction formation and significant upregulation of chaperones Bip and Hsp70 as well as AP-1 proteins c-Fos and JunB, in addition to molecular signatures of skin diseases. Consistently, c-Fos, JunB, Bip and Hsp70 are strikingly higher in keratinocytes of EKV patients than their matched control individuals. Furthermore, a druggable AP-1 inhibitory small molecule suppresses skin phenotype and pathological abnormalities of transgenic Cx31 mice. The study suggests that Cx31 mutant proteins are un/misfolded to cause EKV likely via an AP-1-mediated mechanism and identifies a small molecule with therapeutic potential of the disease. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Carbon chemistry in dense molecular clouds: Theory and observational constraints

NASA Technical Reports Server (NTRS)

Blake, Geoffrey A.

1990-01-01

For the most part, gas phase models of the chemistry of dense molecular clouds predict the abundances of simple species rather well. However, for larger molecules and even for small systems rich in carbon these models often fail spectacularly. Researchers present a brief review of the basic assumptions and results of large scale modeling of the carbon chemistry in dense molecular clouds. Particular attention is to the influence of the gas phase C/O ratio in molecular clouds, and the likely role grains play in maintaining this ratio as clouds evolve from initially diffuse objects to denser cores with associated stellar and planetary formation. Recent spectral line surveys at centimeter and millimeter wavelengths along with selected observations in the submillimeter have now produced an accurate inventory of the gas phase carbon budget in several different types of molecular clouds, though gaps in our knowledge clearly remain. The constraints these observations place on theoretical models of interstellar chemistry can be used to gain insights into why the models fail, and show also which neglected processes must be included in more complete analyses. Looking toward the future, larger molecules are especially difficult to study both experimentally and theoretically in such dense, cold regions, and some new methods are therefore outlined which may ultimately push the detectability of small carbon chains and rings to much heavier species.

Gas heating dynamics during leader inception in long air gaps at atmospheric pressure

NASA Astrophysics Data System (ADS)

Liu, Lipeng; Becerra, Marley

2017-08-01

The inception of leader discharges in long air gaps at atmospheric pressure is simulated with a thermo-hydrodynamic model and a detailed kinetic scheme for N2/O2/H2O mixtures. In order to investigate the effect of humidity, the kinetic scheme includes the most important reactions with the H2O molecule and its derivatives, resulting in a scheme with 45 species and 192 chemical reactions. The heating of a thin plasma channel in front of an anode electrode during the streamer to leader transition is evaluated with a detailed 1D radial model. The analysis includes the simulation of the corresponding streamer bursts, dark periods and aborted leaders that may occur prior to the inception of a propagating leader discharge. The simulations are performed using the time-varying discharge current in two laboratory discharge events of positive polarity reported in the literature as input. Excellent agreement between the simulated and the experimental time variation of the thermal radius for a 1 m rod-plate air gap discharge event reported in the literature has been found. The role of different energy transfer and loss mechanisms prior to the inception of a stable leader is also discussed. It is found that although a small percentage of water molecules can accelerate the vibrational-translational relaxation to some extent, this effect leads to a negligible temperature increase during the streamer-to-leader transition. It is also found that the gas temperature should significantly exceed 2000 K for the transition to lead to the inception of a propagating leader. Otherwise, the strong convection loss produced by the gas expansion during the transition causes a drop in the translational temperature below 2000 K, aborting the incepted leader. Furthermore, it is shown that the assumptions used by the widely-used model of Gallimberti do not hold when evaluating the streamer-to-leader transition.

Selection and Biosensor Application of Aptamers for Small Molecules

PubMed Central

Pfeiffer, Franziska; Mayer, Günter

2016-01-01

Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging. PMID:27379229

Methods to enable the design of bioactive small molecules targeting RNA

PubMed Central

Disney, Matthew D.; Yildirim, Ilyas; Childs-Disney, Jessica L.

2014-01-01

RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including Structure-Activity Relationships Through Sequencing (StARTS), quantitative structure-activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome. PMID:24357181

Methods to enable the design of bioactive small molecules targeting RNA.

PubMed

Disney, Matthew D; Yildirim, Ilyas; Childs-Disney, Jessica L

2014-02-21

RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure-activity relationships through sequencing (StARTS), quantitative structure-activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.

PubMed

Seashore-Ludlow, Brinton; Rees, Matthew G; Cheah, Jaime H; Cokol, Murat; Price, Edmund V; Coletti, Matthew E; Jones, Victor; Bodycombe, Nicole E; Soule, Christian K; Gould, Joshua; Alexander, Benjamin; Li, Ava; Montgomery, Philip; Wawer, Mathias J; Kuru, Nurdan; Kotz, Joanne D; Hon, C Suk-Yee; Munoz, Benito; Liefeld, Ted; Dančík, Vlado; Bittker, Joshua A; Palmer, Michelle; Bradner, James E; Shamji, Alykhan F; Clemons, Paul A; Schreiber, Stuart L

2015-11-01

Identifying genetic alterations that prime a cancer cell to respond to a particular therapeutic agent can facilitate the development of precision cancer medicines. Cancer cell-line (CCL) profiling of small-molecule sensitivity has emerged as an unbiased method to assess the relationships between genetic or cellular features of CCLs and small-molecule response. Here, we developed annotated cluster multidimensional enrichment analysis to explore the associations between groups of small molecules and groups of CCLs in a new, quantitative sensitivity dataset. This analysis reveals insights into small-molecule mechanisms of action, and genomic features that associate with CCL response to small-molecule treatment. We are able to recapitulate known relationships between FDA-approved therapies and cancer dependencies and to uncover new relationships, including for KRAS-mutant cancers and neuroblastoma. To enable the cancer community to explore these data, and to generate novel hypotheses, we created an updated version of the Cancer Therapeutic Response Portal (CTRP v2). We present the largest CCL sensitivity dataset yet available, and an analysis method integrating information from multiple CCLs and multiple small molecules to identify CCL response predictors robustly. We updated the CTRP to enable the cancer research community to leverage these data and analyses. ©2015 American Association for Cancer Research.

Nanoscale patterning of STIM1 and Orai1 during store-operated Ca2+ entry.

PubMed

Perni, Stefano; Dynes, Joseph L; Yeromin, Andriy V; Cahalan, Michael D; Franzini-Armstrong, Clara

2015-10-06

Stromal interacting molecule (STIM) and Orai proteins constitute the core machinery of store-operated calcium entry. We used transmission and freeze-fracture electron microscopy to visualize STIM1 and Orai1 at endoplasmic reticulum (ER)-plasma membrane (PM) junctions in HEK 293 cells. Compared with control cells, thin sections of STIM1-transfected cells possessed far more ER elements, which took the form of complex stackable cisternae and labyrinthine structures adjoining the PM at junctional couplings (JCs). JC formation required STIM1 expression but not store depletion, induced here by thapsigargin (TG). Extended molecules, indicative of STIM1, decorated the cytoplasmic surface of ER, bridged a 12-nm ER-PM gap, and showed clear rearrangement into small clusters following TG treatment. Freeze-fracture replicas of the PM of Orai1-transfected cells showed extensive domains packed with characteristic "particles"; TG treatment led to aggregation of these particles into sharply delimited "puncta" positioned upon raised membrane subdomains. The size and spacing of Orai1 channels were consistent with the Orai crystal structure, and stoichiometry was unchanged by store depletion, coexpression with STIM1, or an Orai1 mutation (L273D) affecting STIM1 association. Although the arrangement of Orai1 channels in puncta was substantially unstructured, a portion of channels were spaced at ∼15 nm. Monte Carlo analysis supported a nonrandom distribution for a portion of channels spaced at ∼15 nm. These images offer dramatic, direct views of STIM1 aggregation and Orai1 clustering in store-depleted cells and provide evidence for the interaction of a single Orai1 channel with small clusters of STIM1 molecules.

Nanoscale patterning of STIM1 and Orai1 during store-operated Ca2+ entry

PubMed Central

Perni, Stefano; Dynes, Joseph L.; Yeromin, Andriy V.; Cahalan, Michael D.; Franzini-Armstrong, Clara

2015-01-01

Stromal interacting molecule (STIM) and Orai proteins constitute the core machinery of store-operated calcium entry. We used transmission and freeze–fracture electron microscopy to visualize STIM1 and Orai1 at endoplasmic reticulum (ER)–plasma membrane (PM) junctions in HEK 293 cells. Compared with control cells, thin sections of STIM1-transfected cells possessed far more ER elements, which took the form of complex stackable cisternae and labyrinthine structures adjoining the PM at junctional couplings (JCs). JC formation required STIM1 expression but not store depletion, induced here by thapsigargin (TG). Extended molecules, indicative of STIM1, decorated the cytoplasmic surface of ER, bridged a 12-nm ER-PM gap, and showed clear rearrangement into small clusters following TG treatment. Freeze–fracture replicas of the PM of Orai1-transfected cells showed extensive domains packed with characteristic “particles”; TG treatment led to aggregation of these particles into sharply delimited “puncta” positioned upon raised membrane subdomains. The size and spacing of Orai1 channels were consistent with the Orai crystal structure, and stoichiometry was unchanged by store depletion, coexpression with STIM1, or an Orai1 mutation (L273D) affecting STIM1 association. Although the arrangement of Orai1 channels in puncta was substantially unstructured, a portion of channels were spaced at ∼15 nm. Monte Carlo analysis supported a nonrandom distribution for a portion of channels spaced at ∼15 nm. These images offer dramatic, direct views of STIM1 aggregation and Orai1 clustering in store-depleted cells and provide evidence for the interaction of a single Orai1 channel with small clusters of STIM1 molecules. PMID:26351694

Measles Virus Fusion Protein: Structure, Function and Inhibition

PubMed Central

Plattet, Philippe; Alves, Lisa; Herren, Michael; Aguilar, Hector C.

2016-01-01

Measles virus (MeV), a highly contagious member of the Paramyxoviridae family, causes measles in humans. The Paramyxoviridae family of negative single-stranded enveloped viruses includes several important human and animal pathogens, with MeV causing approximately 120,000 deaths annually. MeV and canine distemper virus (CDV)-mediated diseases can be prevented by vaccination. However, sub-optimal vaccine delivery continues to foster MeV outbreaks. Post-exposure prophylaxis with antivirals has been proposed as a novel strategy to complement vaccination programs by filling herd immunity gaps. Recent research has shown that membrane fusion induced by the morbillivirus glycoproteins is the first critical step for viral entry and infection, and determines cell pathology and disease outcome. Our molecular understanding of morbillivirus-associated membrane fusion has greatly progressed towards the feasibility to control this process by treating the fusion glycoprotein with inhibitory molecules. Current approaches to develop anti-membrane fusion drugs and our knowledge on drug resistance mechanisms strongly suggest that combined therapies will be a prerequisite. Thus, discovery of additional anti-fusion and/or anti-attachment protein small-molecule compounds may eventually translate into realistic therapeutic options. PMID:27110811

Measles Virus Fusion Protein: Structure, Function and Inhibition.

PubMed

Plattet, Philippe; Alves, Lisa; Herren, Michael; Aguilar, Hector C

2016-04-21

Measles virus (MeV), a highly contagious member of the Paramyxoviridae family, causes measles in humans. The Paramyxoviridae family of negative single-stranded enveloped viruses includes several important human and animal pathogens, with MeV causing approximately 120,000 deaths annually. MeV and canine distemper virus (CDV)-mediated diseases can be prevented by vaccination. However, sub-optimal vaccine delivery continues to foster MeV outbreaks. Post-exposure prophylaxis with antivirals has been proposed as a novel strategy to complement vaccination programs by filling herd immunity gaps. Recent research has shown that membrane fusion induced by the morbillivirus glycoproteins is the first critical step for viral entry and infection, and determines cell pathology and disease outcome. Our molecular understanding of morbillivirus-associated membrane fusion has greatly progressed towards the feasibility to control this process by treating the fusion glycoprotein with inhibitory molecules. Current approaches to develop anti-membrane fusion drugs and our knowledge on drug resistance mechanisms strongly suggest that combined therapies will be a prerequisite. Thus, discovery of additional anti-fusion and/or anti-attachment protein small-molecule compounds may eventually translate into realistic therapeutic options.

Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage

PubMed Central

Lobo, Elena; Dalling, James W.

2014-01-01

Treefall gaps play an important role in tropical forest dynamics and in determining above-ground biomass (AGB). However, our understanding of gap disturbance regimes is largely based either on surveys of forest plots that are small relative to spatial variation in gap disturbance, or on satellite imagery, which cannot accurately detect small gaps. We used high-resolution light detection and ranging data from a 1500 ha forest in Panama to: (i) determine how gap disturbance parameters are influenced by study area size, and the criteria used to define gaps; and (ii) to evaluate how accurately previous ground-based canopy height sampling can determine the size and location of gaps. We found that plot-scale disturbance parameters frequently differed significantly from those measured at the landscape-level, and that canopy height thresholds used to define gaps strongly influenced the gap-size distribution, an important metric influencing AGB. Furthermore, simulated ground surveys of canopy height frequently misrepresented the true location of gaps, which may affect conclusions about how relatively small canopy gaps affect successional processes and contribute to the maintenance of diversity. Across site comparisons need to consider how gap definition, scale and spatial resolution affect characterizations of gap disturbance, and its inferred importance for carbon storage and community composition. PMID:24452032

Probing the energetics of organic–nanoparticle interactions of ethanol on calcite

PubMed Central

Wu, Di; Navrotsky, Alexandra

2015-01-01

Knowing the nature of interactions between small organic molecules and surfaces of nanoparticles (NP) is crucial for fundamental understanding of natural phenomena and engineering processes. Herein, we report direct adsorption enthalpy measurement of ethanol on a series of calcite nanocrystals, with the aim of mimicking organic–NP interactions in various environments. The energetics suggests a spectrum of adsorption events as a function of coverage: strongest initial chemisorption on active sites on fresh calcite surfaces, followed by major chemical binding to form an ethanol monolayer and, subsequently, very weak, near-zero energy, physisorption. These thermochemical observations directly support a structure where the ethanol monolayer is bonded to the calcite surface through its polar hydroxyl group, leaving the hydrophobic ends of the ethanol molecules to interact only weakly with the next layer of adsorbing ethanol and resulting in a spatial gap with low ethanol density between the monolayer and subsequent added ethanol molecules, as predicted by molecular dynamics and density functional calculations. Such an ordered assembly of ethanol on calcite NP is analogous to, although less strongly bonded than, a capping layer of organics intentionally introduced during NP synthesis, and suggests a continuous variation of surface structure depending on molecular chemistry, ranging from largely disordered surface layers to ordered layers that nevertheless are mobile and can rearrange or be displaced by other molecules to strongly bonded immobile organic capping layers. These differences in surface structure will affect chemical reactions, including the further nucleation and growth of nanocrystals on organic ligand-capped surfaces. PMID:25870281

DFT study of adsorption of picric acid molecule on the surface of single-walled ZnO nanotube; as potential new chemical sensor

NASA Astrophysics Data System (ADS)

Farmanzadeh, Davood; Tabari, Leila

2015-01-01

Using density functional theory (DFT), we have investigated the adsorption of picric acid (PA) molecule on the surface of (8,0) single-walled ZnO nanotube (ZnONT). The results show that the PA molecule can be chemisorbed on the surface of ZnONT with adsorption energies of -82.01 and -75.26 kJ/mol in gas and aqueous phase, respectively. Frontier molecular orbital analysis show that HOMO/LUMO gap of ZnONT reduces from 1.66 and 1.75 eV in the pristine nanotube to 0.83 and 0.72 eV in PA-adsorbed form in gas and aqueous phase, respectively. It suggests that the process can affect the electronic properties of the studied nanotube which would lead to its conductance change upon the adsorption of PA molecule. The modifying effect on the electrical conductance of ZnONT underlies the working mechanism of gas sensors for detecting the PA molecules. Analyses of the adsorption behavior of the electrically charged ZnONT toward PA molecule in the gas phase show that the PA molecule can be strongly adsorbed on the negatively charged ZnONT surface with significant adsorption energy (-135.1 kJ/mol). However, from the HOMO/LUMO gap changes, it can be concluded that the positive ZnONT might sensitively detect the PA molecule in comparison to the negative tube. These results can provide helpful information for experimental investigation to develop novel nanotube-based sensors.

Identification of a Broad-Spectrum Antiviral Small Molecule against Severe Acute Respiratory Syndrome Coronavirus and Ebola, Hendra, and Nipah Viruses by Using a Novel High-Throughput Screening Assay

PubMed Central

Elshabrawy, Hatem A.; Fan, Jilao; Haddad, Christine S.; Ratia, Kiira; Broder, Christopher C.; Caffrey, Michael

2014-01-01

ABSTRACT Severe acute respiratory syndrome coronavirus (SARS-CoV) and Ebola, Hendra, and Nipah viruses are members of different viral families and are known causative agents of fatal viral diseases. These viruses depend on cathepsin L for entry into their target cells. The viral glycoproteins need to be primed by protease cleavage, rendering them active for fusion with the host cell membrane. In this study, we developed a novel high-throughput screening assay based on peptides, derived from the glycoproteins of the aforementioned viruses, which contain the cathepsin L cleavage site. We screened a library of 5,000 small molecules and discovered a small molecule that can inhibit the cathepsin L cleavage of all viral peptides with minimal inhibition of cleavage of a host protein-derived peptide (pro-neuropeptide Y). The small molecule inhibited the entry of all pseudotyped viruses in vitro and the cleavage of SARS-CoV spike glycoprotein in an in vitro cleavage assay. In addition, the Hendra and Nipah virus fusion glycoproteins were not cleaved in the presence of the small molecule in a cell-based cleavage assay. Furthermore, we demonstrate that the small molecule is a mixed inhibitor of cathepsin L. Our broad-spectrum antiviral small molecule appears to be an ideal candidate for future optimization and development into a potent antiviral against SARS-CoV and Ebola, Hendra, and Nipah viruses. IMPORTANCE We developed a novel high-throughput screening assay to identify small molecules that can prevent cathepsin L cleavage of viral glycoproteins derived from SARS-CoV and Ebola, Hendra, and Nipah viruses that are required for their entry into the host cell. We identified a novel broad-spectrum small molecule that could block cathepsin L-mediated cleavage and thus inhibit the entry of pseudotypes bearing the glycoprotein derived from SARS-CoV or Ebola, Hendra, or Nipah virus. The small molecule can be further optimized and developed into a potent broad-spectrum antiviral drug. PMID:24501399

Identification of a broad-spectrum antiviral small molecule against severe acute respiratory syndrome coronavirus and Ebola, Hendra, and Nipah viruses by using a novel high-throughput screening assay.

PubMed

Elshabrawy, Hatem A; Fan, Jilao; Haddad, Christine S; Ratia, Kiira; Broder, Christopher C; Caffrey, Michael; Prabhakar, Bellur S

2014-04-01

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Ebola, Hendra, and Nipah viruses are members of different viral families and are known causative agents of fatal viral diseases. These viruses depend on cathepsin L for entry into their target cells. The viral glycoproteins need to be primed by protease cleavage, rendering them active for fusion with the host cell membrane. In this study, we developed a novel high-throughput screening assay based on peptides, derived from the glycoproteins of the aforementioned viruses, which contain the cathepsin L cleavage site. We screened a library of 5,000 small molecules and discovered a small molecule that can inhibit the cathepsin L cleavage of all viral peptides with minimal inhibition of cleavage of a host protein-derived peptide (pro-neuropeptide Y). The small molecule inhibited the entry of all pseudotyped viruses in vitro and the cleavage of SARS-CoV spike glycoprotein in an in vitro cleavage assay. In addition, the Hendra and Nipah virus fusion glycoproteins were not cleaved in the presence of the small molecule in a cell-based cleavage assay. Furthermore, we demonstrate that the small molecule is a mixed inhibitor of cathepsin L. Our broad-spectrum antiviral small molecule appears to be an ideal candidate for future optimization and development into a potent antiviral against SARS-CoV and Ebola, Hendra, and Nipah viruses. We developed a novel high-throughput screening assay to identify small molecules that can prevent cathepsin L cleavage of viral glycoproteins derived from SARS-CoV and Ebola, Hendra, and Nipah viruses that are required for their entry into the host cell. We identified a novel broad-spectrum small molecule that could block cathepsin L-mediated cleavage and thus inhibit the entry of pseudotypes bearing the glycoprotein derived from SARS-CoV or Ebola, Hendra, or Nipah virus. The small molecule can be further optimized and developed into a potent broad-spectrum antiviral drug.

Dynamic traversal of high bumps and large gaps by a small legged robot

NASA Astrophysics Data System (ADS)

Gart, Sean; Winey, Nastasia; de La Tijera Obert, Rafael; Li, Chen

Small animals encounter and negotiate diverse obstacles comparable in size or larger than themselves. In recent experiments, we found that cockroaches can dynamically traverse bumps up to 4 times hip height and gaps up to 1 body length. To better understand the physics that governs these locomotor transitions, we studied a small six-legged robot negotiating high bumps and large gaps and compared it to animal observations. We found that the robot was able to traverse bumps as large as 1 hip height and gaps as wide as 0.5 body length. For the bump, the robot often climbed over to traverse when initial body yaw was small, but was often deflected laterally and failed to traverse when initial body yaw was large. A simple locomotion energy landscape model explained these observations. For the gap, traversal probability decreased with gap width, which was well explained by a simple Lagrangian model of a forward-moving rigid body falling over the gap edge. For both the bump and the gap, animal performance far exceeded that of the robot, likely due to their relatively higher running speeds and larger rotational oscillations prior to and during obstacle traversal. Differences between animal and robot obstacle negotiation behaviors revealed that animals used active strategies to overcome potential energy barriers.

Closing the Gap: Meeting the Small Business Training Challenge in Connecticut.

ERIC Educational Resources Information Center

Harwood, Richard C.

The training needs of Connecticut's small businesses and their employees are not being adequately met. Small businesses face an economy placing increasing demands on them: a worsening labor shortage, an aging work force, and changing skills in the workplace. Gaps in private and public sector training programs impede small businesses from meeting…

Automated measurement of pulmonary emphysema and small airway remodeling in cigarette smoke-exposed mice.

PubMed

Laucho-Contreras, Maria E; Taylor, Katherine L; Mahadeva, Ravi; Boukedes, Steve S; Owen, Caroline A

2015-01-16

COPD is projected to be the third most common cause of mortality world-wide by 2020((1)). Animal models of COPD are used to identify molecules that contribute to the disease process and to test the efficacy of novel therapies for COPD. Researchers use a number of models of COPD employing different species including rodents, guinea-pigs, rabbits, and dogs((2)). However, the most widely-used model is that in which mice are exposed to cigarette smoke. Mice are an especially useful species in which to model COPD because their genome can readily be manipulated to generate animals that are either deficient in, or over-express individual proteins. Studies of gene-targeted mice that have been exposed to cigarette smoke have provided valuable information about the contributions of individual molecules to different lung pathologies in COPD((3-5)). Most studies have focused on pathways involved in emphysema development which contributes to the airflow obstruction that is characteristic of COPD. However, small airway fibrosis also contributes significantly to airflow obstruction in human COPD patients((6)), but much less is known about the pathogenesis of this lesion in smoke-exposed animals. To address this knowledge gap, this protocol quantifies both emphysema development and small airway fibrosis in smoke-exposed mice. This protocol exposes mice to CS using a whole-body exposure technique, then measures respiratory mechanics in the mice, inflates the lungs of mice to a standard pressure, and fixes the lungs in formalin. The researcher then stains the lung sections with either Gill's stain to measure the mean alveolar chord length (as a readout of emphysema severity) or Masson's trichrome stain to measure deposition of extracellular matrix (ECM) proteins around small airways (as a readout of small airway fibrosis). Studies of the effects of molecular pathways on both of these lung pathologies will lead to a better understanding of the pathogenesis of COPD.

Recent Developments in β-Cell Differentiation of Pluripotent Stem Cells Induced by Small and Large Molecules

PubMed Central

Kumar, S. Suresh; Alarfaj, Abdullah A.; Munusamy, Murugan A.; Singh, A. J. A. Ranjith; Peng, I-Chia; Priya, Sivan Padma; Hamat, Rukman Awang; Higuchi, Akon

2014-01-01

Human pluripotent stem cells, including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), hold promise as novel therapeutic tools for diabetes treatment because of their self-renewal capacity and ability to differentiate into beta (β)-cells. Small and large molecules play important roles in each stage of β-cell differentiation from both hESCs and hiPSCs. The small and large molecules that are described in this review have significantly advanced efforts to cure diabetic disease. Lately, effective protocols have been implemented to induce hESCs and human mesenchymal stem cells (hMSCs) to differentiate into functional β-cells. Several small molecules, proteins, and growth factors promote pancreatic differentiation from hESCs and hMSCs. These small molecules (e.g., cyclopamine, wortmannin, retinoic acid, and sodium butyrate) and large molecules (e.g. activin A, betacellulin, bone morphogentic protein (BMP4), epidermal growth factor (EGF), fibroblast growth factor (FGF), keratinocyte growth factor (KGF), hepatocyte growth factor (HGF), noggin, transforming growth factor (TGF-α), and WNT3A) are thought to contribute from the initial stages of definitive endoderm formation to the final stages of maturation of functional endocrine cells. We discuss the importance of such small and large molecules in uniquely optimized protocols of β-cell differentiation from stem cells. A global understanding of various small and large molecules and their functions will help to establish an efficient protocol for β-cell differentiation. PMID:25526563

High Throughput, Label-free Screening Small Molecule Compound Libraries for Protein-Ligands using Combination of Small Molecule Microarrays and a Special Ellipsometry-based Optical Scanner.

PubMed

Landry, James P; Fei, Yiyan; Zhu, X D

2011-12-01

Small-molecule compounds remain the major source of therapeutic and preventative drugs. Developing new drugs against a protein target often requires screening large collections of compounds with diverse structures for ligands or ligand fragments that exhibit sufficiently affinity and desirable inhibition effect on the target before further optimization and development. Since the number of small molecule compounds is large, high-throughput screening (HTS) methods are needed. Small-molecule microarrays (SMM) on a solid support in combination with a suitable binding assay form a viable HTS platform. We demonstrate that by combining an oblique-incidence reflectivity difference optical scanner with SMM we can screen 10,000 small-molecule compounds on a single glass slide for protein ligands without fluorescence labeling. Furthermore using such a label-free assay platform we can simultaneously acquire binding curves of a solution-phase protein to over 10,000 immobilized compounds, thus enabling full characterization of protein-ligand interactions over a wide range of affinity constants.

Delivery of small molecules for bone regenerative engineering: preclinical studies and potential clinical applications.

PubMed

Laurencin, Cato T; Ashe, Keshia M; Henry, Nicole; Kan, Ho Man; Lo, Kevin W-H

2014-06-01

Stimulation of bone regeneration using growth factors is a promising approach for musculoskeletal regenerative engineering. However, common limitations with protein growth factors, such as high manufacturing costs, protein instability, contamination issues, and unwanted immunogenic responses of the host reduce potential clinical applications. New strategies for bone regeneration that involve inexpensive and stable small molecules can obviate these problems and have a significant impact on the treatment of skeletal injury and diseases. Over the past decade, a large number of small molecules with the potential of regenerating skeletal tissue have been reported in the literature. Here, we review this literature, paying specific attention to the prospects for small molecule-based bone-regenerative engineering. We also review the preclinical study of small molecules associated with bone regeneration. Copyright © 2014 Elsevier Ltd. All rights reserved.

Small molecule annotation for the Protein Data Bank

PubMed Central

Sen, Sanchayita; Young, Jasmine; Berrisford, John M.; Chen, Minyu; Conroy, Matthew J.; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P.; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A.

2014-01-01

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. PMID:25425036

Small molecule annotation for the Protein Data Bank.

PubMed

Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

2014-01-01

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. © The Author(s) 2014. Published by Oxford University Press.

Developing an Efficient and General Strategy for Immobilization of Small Molecules onto Microarrays Using Isocyanate Chemistry.

PubMed

Zhu, Chenggang; Zhu, Xiangdong; Landry, James P; Cui, Zhaomeng; Li, Quanfu; Dang, Yongjun; Mi, Lan; Zheng, Fengyun; Fei, Yiyan

2016-03-16

Small-molecule microarray (SMM) is an effective platform for identifying lead compounds from large collections of small molecules in drug discovery, and efficient immobilization of molecular compounds is a pre-requisite for the success of such a platform. On an isocyanate functionalized surface, we studied the dependence of immobilization efficiency on chemical residues on molecular compounds, terminal residues on isocyanate functionalized surface, lengths of spacer molecules, and post-printing treatment conditions, and we identified a set of optimized conditions that enable us to immobilize small molecules with significantly improved efficiencies, particularly for those molecules with carboxylic acid residues that are known to have low isocyanate reactivity. We fabricated microarrays of 3375 bioactive compounds on isocyanate functionalized glass slides under these optimized conditions and confirmed that immobilization percentage is over 73%.

Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules

NASA Astrophysics Data System (ADS)

Veetil, Aneesh T.; Chakraborty, Kasturi; Xiao, Kangni; Minter, Myles R.; Sisodia, Sangram S.; Krishnan, Yamuna

2017-12-01

Achieving triggered release of small molecules with spatial and temporal precision at designated cells within an organism remains a challenge. By combining a cell-targetable, icosahedral DNA-nanocapsule loaded with photoresponsive polymers, we show cytosolic delivery of small molecules with the spatial resolution of single endosomes in specific cells in Caenorhabditis elegans. Our technology can report on the extent of small molecules released after photoactivation as well as pinpoint the location at which uncaging of the molecules occurred. We apply this technology to release dehydroepiandrosterone (DHEA), a neurosteroid that promotes neurogenesis and neuron survival, and determined the timescale of neuronal activation by DHEA, using light-induced release of DHEA from targeted DNA nanocapsules. Importantly, sequestration inside the DNA capsule prevents photocaged DHEA from activating neurons prematurely. Our methodology can in principle be generalized to diverse neurostimulatory molecules.

Asphaltenes as new objects for nanoelectronics

NASA Astrophysics Data System (ADS)

Dolomatov, M. Yu; Petrov, A. M.; Bakhtizin, R. Z.; Dolomatova, M. M.; Khairudinov, I. R.; Shutkova, S. A.; Kovaleva, E. A.; Paymurzina, N. Kh

2017-05-01

Abstract. Modern carbon nanomaterials (carbon nanotubes, graphenes, fullerenes, polycyclic molecules) are products of rather complicated technologies. Therefore development of new not expensive materials on the basis of natural substances, in particular high-molecular compounds of oil - asphaltenes, is actual for nanoelectronics. Asphaltenes are complex materials that are found in crude oil, bitumen and high-boiling hydrocarbons distillates. Usually asphaltenes are composed mainly of polyaromatic carbon with a small amount of vanadium and nickel, which are in porphyrin structures. Molecules of asphaltenes may contain 5-10-member benzene and naphthenic rings in their structure and also have paramagnetic centers. A variety of techniques: electronic phenomenological spectroscopy (EPS), atomic force microscopy (AFM) and quantum chemistry calculations were used to define the structure of oil asphaltenes. It was supposed that asphaltene fraction is a strong donor (ionization potential 4.10-6.70 eV) and an acceptor (electron affinity 1.80-2.50 eV). The structures of asphaltenes fragments were calculated by RHF-6-31G** methods. AFM images of asphaltenes obtained from crude oil showed the presence of structure fragments ranged from 3 to 10 nm, disposed to strong intermolecular interactions. We used doped compounds for formation of wide band gap amorphous semiconductors from a concentrates of asphaltens. Changes of conductivity in dispersed petroleum systems (DPS) were studied during a pyrolysis at 500 K. The numerous experiments defined of conductivity testify about phase transitions dielectric - semiconductor in DPS for range of 360 - 400 K. The main conclusion is paramagnetic phase of asphaltenes is organic amorphous wide band gap semiconductor. Besides this substance can be consider as an organic spin glasses.

Small-size controlled vacuum spark-gap in an external magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asyunin, V. I., E-mail: asvi@mail.ru; Davydov, S. G.; Dolgov, A. N., E-mail: alnikdolgov@mail.ru

2015-02-15

It is demonstrated that the operation of a small-size controlled spark-gap can be controlled by applying a uniform external magnetic field. It is shown that the magnetic field of such a simple configuration efficiently suppresses the effect of localization of the discharge current after multiple actuations of the spark-gap.

Exploring biology with small organic molecules

PubMed Central

Stockwell, Brent R.

2011-01-01

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore ‘biological-activity space’. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars — uncharted territory is explored using a system of coordinates that describes where each new feature lies. PMID:15602550

Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas.

PubMed

Simoncelli, Sabrina; Roller, Eva-Maria; Urban, Patrick; Schreiber, Robert; Turberfield, Andrew J; Liedl, Tim; Lohmüller, Theobald

2016-11-22

DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.

BN-C Hybrid Nanoribbons as Gas Sensors

NASA Astrophysics Data System (ADS)

Darvishi Gilan, Mahdi; Chegel, Raad

2018-02-01

The effects of carbon monoxide (CO) and ammonia (NH3) molecules adsorption on the various composites of boron nitride and graphene BN-C hybrid nanoribbons are investigated using the non-equilibrium Green's function (NEGF) technique based on density functional theory (DFT). The effects of adsorption with possible random configurations on the average of the density of states (DOS), transmission coefficient, and the current-voltage ( I- V) characteristics are calculated. The results indicate that, by embedding armchair graphene nanoribbon (AGNR) with boron nitride nanoribbon (BNNR), the various electronic properties can be observed after gas molecule adsorption. The electronic structure and gap of hybrids system is modified due to gas adsorption, and the systems act like the n-type semiconductor by NH3 molecule adsorption. The hybrid structures due to their tunable band gap are better candidates for gas detecting compared to the pristine BNNRs and AGNRs.

Small Moon Makes Big Waves

NASA Image and Video Library

2012-12-31

Saturn small moon Daphnis is caught in the act of raising waves on the edges of the Keeler gap, which is the thin dark band in the left half of the image. Waves like these allow scientists to locate small moons in gaps and measure their masses.

Morphological study on small molecule acceptor-based organic solar cells with efficiencies beyond 7% (Presentation Recording)

NASA Astrophysics Data System (ADS)

Ma, Wei; Yan, He

2015-10-01

Despite the essential role of fullerenes in achieving best-performance organic solar cells (OSCs), fullerene acceptors have several drawbacks including poor light absorption, high-cost production and purification. For this reason, small molecule acceptor (SMA)-based OSCs have attracted much attention due to the easy tunability of electronic and optical properties of SMA materials. In this study, polymers with temperature dependent aggregation behaviors are combined with various small molecule acceptor materials, which lead to impressive power conversion efficiencies of up to 7.3%. The morphological and aggregation properties of the polymer:small molecule blends are studied in details. It is found that the temperature-dependent aggregation behavior of polymers allows for the processing of the polymer solutions at moderately elevated temperature, and more importantly, controlled aggregation and strong crystallization of the polymer during the film cooling and drying process. This results in a well-controlled and near-ideal polymer:small molecule morphology that is controlled by polymer aggregation during warm casting and thus insensitive to the choice of small molecules. As a result, several cases of highly efficient (PCE between 6-7.3%) SMA OSCs are achieved. The second part of this presentation will describe the morphology of a new small molecule acceptor with a unique 3D structure. The relationship between molecular structure and morphology is revealed.

Identification of small molecule inhibitors of cytokinesis and single cell wound repair

PubMed Central

Clark, Andrew G.; Sider, Jenny R.; Verbrugghe, Koen; Fenteany, Gabriel; von Dassow, George; Bement, William M.

2013-01-01

Screening of small molecule libraries offers the potential to identify compounds that inhibit specific biological processes and, ultimately, to identify macromolecules that are important players in such processes. To date, however, most screens of small molecule libraries have focused on identification of compounds that inhibit known proteins or particular steps in a given process, and have emphasized automated primary screens. Here we have used “low tech” in vivo primary screens to identify small molecules that inhibit both cytokinesis and single cell wound repair, two complex cellular processes that possess many common features. The “diversity set”, an ordered array of 1990 compounds available from the National Cancer Institute, was screened in parallel to identify compounds that inhibit cytokinesis in D. excentricus (sand dollar) embryos and single cell wound repair in X. laevis (frog) oocytes. Two small molecules were thus identified: Sph1 and Sph2. Sph1 reduces Rho activation in wound repair and suppresses formation of the spindle midzone during cytokinesis. Sph2 also reduces Rho activation in wound repair and may inhibit cytokinesis by blocking membrane fusion. The results identify two small molecules of interest for analysis of wound repair and cytokinesis, reveal that these processes are more similar than often realized and reveal the potential power of low tech screens of small molecule libraries for analysis of complex cellular processes. PMID:23125193

The influence of conjugated alkynyl(aryl) surface groups on the optical properties of silicon nanocrystals: photoluminescence through in-gap states.

PubMed

Angı, Arzu; Sinelnikov, Regina; Heenen, Hendrik H; Meldrum, Al; Veinot, Jonathan G C; Scheurer, Christoph; Reuter, Karsten; Ashkenazy, Or; Azulay, Doron; Balberg, Isaac; Millo, Oded; Rieger, Bernhard

2018-08-31

Developing new methods, other than size and shape, for controlling the optoelectronic properties of semiconductor nanocrystals is a highly desired target. Here we demonstrate that the photoluminescence (PL) of silicon nanocrystals (SiNCs) can be tuned in the range 685-800 nm solely via surface functionalization with alkynyl(aryl) (phenylacetylene, 2-ethynylnaphthalene, 2-ethynyl-5-hexylthiophene) surface groups. Scanning tunneling microscopy/spectroscopy on single nanocrystals revealed the formation of new in-gap states adjacent to the conduction band edge of the functionalized SiNCs. PL red-shifts were attributed to emission through these in-gap states, which reduce the effective band gap for the electron-hole recombination process. The observed in-gap states can be associated with new interface states formed via (-Si-C≡C-) bonds in combination with conjugated molecules as indicated by ab initio calculations. In contrast to alkynyl(aryl)s, the formation of in-gap states and shifts in PL maximum of the SiNCs were not observed with aryl (phenyl, naphthalene, 2-hexylthiophene) and alkynyl (1-dodecyne) surface groups. These outcomes show that surface functionalization with alkynyl(aryl) molecules is a valuable tool to control the electronic structure and optical properties of SiNCs via tuneable interface states, which may enhance the performance of SiNCs in semiconductor devices.

Possible involvement of gap junctions in the barrier function of tight junctions of brain and lung endothelial cells.

PubMed

Nagasawa, Kunihiko; Chiba, Hideki; Fujita, Hiroki; Kojima, Takashi; Saito, Tsuyoshi; Endo, Toshiaki; Sawada, Norimasa

2006-07-01

Gap-junction plaques are often observed with tight-junction strands of vascular endothelial cells but the molecular interaction and functional relationships between these two junctions remain obscure. We herein show that gap-junction proteins connexin40 (Cx40) and Cx43 are colocalized and coprecipitated with tight-junction molecules occludin, claudin-5, and ZO-1 in porcine blood-brain barrier (BBB) endothelial cells. Gap junction blockers 18beta-glycyrrhetinic acid (18beta-GA) and oleamide (OA) did not influence expression of Cx40, Cx43, occludin, claudin-5, junctional adhesion molecule (JAM)-A, JAM-B, JAM-C, or ZO-1, or their subcellular localization in the porcine BBB endothelial cells. In contrast, these gap-junction blocking agents inhibited the barrier function of tight junctions in cells, determined by measurement of transendothelial electrical resistance and paracellular flux of mannitol and inulin. 18beta-GA also significantly reduced the barrier property in rat lung endothelial (RLE) cells expressing doxycycline-induced claudin-1, but did not change the interaction between Cx43 and either claudin-1 or ZO-1, nor their expression levels or subcellular distribution. These findings suggest that Cx40- and/or Cx43-based gap junctions might be required to maintain the endothelial barrier function without altering the expression and localization of the tight-junction components analyzed. Copyright 2006 Wiley-Liss, Inc.

Small band gap superlattices as intrinsic long wavelength infrared detector materials

NASA Technical Reports Server (NTRS)

Smith, Darryl L.; Mailhiot, C.

1990-01-01

Intrinsic long wavelength (lambda greater than or equal to 10 microns) infrared (IR) detectors are currently made from the alloy (Hg, Cd)Te. There is one parameter, the alloy composition, which can be varied to control the properties of this material. The parameter is chosen to set the band gap (cut-off wavelength). The (Hg, Cd)Te alloy has the zincblend crystal structure. Consequently, the electron and light-hole effective masses are essentially inversely proportional to the band gap. As a result, the electron and light-hole effective masses are very small (M sub(exp asterisk)/M sub o approx. M sub Ih/M sub o approx. less than 0.01) whereas the heavy-hole effective mass is ordinary size (M sub hh(exp asterisk)/M sub o approx. 0.4) for the alloy compositions required for intrinsic long wavelength IR detection. This combination of effective masses leads to rather easy tunneling and relatively large Auger transition rates. These are undesirable characteristics, which must be designed around, of an IR detector material. They follow directly from the fact that (Hg, Cd)Te has the zincblend crystal structure and a small band gap. In small band gap superlattices, such as HgTe/CdTe, In(As, Sb)/InSb and InAs/(Ga,In)Sb, the band gap is determined by the superlattice layer thicknesses as well as by the alloy composition (for superlattices containing an alloy). The effective masses are not directly related to the band gap and can be separately varied. In addition, both strain and quantum confinement can be used to split the light-hole band away from the valence band maximum. These band structure engineering options can be used to reduce tunneling probabilities and Auger transition rates compared with a small band gap zincblend structure material. Researchers discuss the different band structure engineering options for the various classes of small band gap superlattices.

High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance.

PubMed

Wambaugh, Morgan A; Shakya, Viplendra P S; Lewis, Adam J; Mulvey, Matthew A; Brown, Jessica C S

2017-06-01

Antibiotic-resistant infections kill approximately 23,000 people and cost $20,000,000,000 each year in the United States alone despite the widespread use of small-molecule antimicrobial combination therapy. Antibiotic combinations typically have an additive effect: the efficacy of the combination matches the sum of the efficacies of each antibiotic when used alone. Small molecules can also act synergistically when the efficacy of the combination is greater than the additive efficacy. However, synergistic combinations are rare and have been historically difficult to identify. High-throughput identification of synergistic pairs is limited by the scale of potential combinations: a modest collection of 1,000 small molecules involves 1 million pairwise combinations. Here, we describe a high-throughput method for rapid identification of synergistic small-molecule pairs, the overlap2 method (O2M). O2M extracts patterns from chemical-genetic datasets, which are created when a collection of mutants is grown in the presence of hundreds of different small molecules, producing a precise set of phenotypes induced by each small molecule across the mutant set. The identification of mutants that show the same phenotype when treated with known synergistic molecules allows us to pinpoint additional molecule combinations that also act synergistically. As a proof of concept, we focus on combinations with the antibiotics trimethoprim and sulfamethizole, which had been standard treatment against urinary tract infections until widespread resistance decreased efficacy. Using O2M, we screened a library of 2,000 small molecules and identified several that synergize with the antibiotic trimethoprim and/or sulfamethizole. The most potent of these synergistic interactions is with the antiviral drug azidothymidine (AZT). We then demonstrate that understanding the molecular mechanism underlying small-molecule synergistic interactions allows the rational design of additional combinations that bypass drug resistance. Trimethoprim and sulfamethizole are both folate biosynthesis inhibitors. We find that this activity disrupts nucleotide homeostasis, which blocks DNA replication in the presence of AZT. Building on these data, we show that other small molecules that disrupt nucleotide homeostasis through other mechanisms (hydroxyurea and floxuridine) also act synergistically with AZT. These novel combinations inhibit the growth and virulence of trimethoprim-resistant clinical Escherichia coli and Klebsiella pneumoniae isolates, suggesting that they may be able to be rapidly advanced into clinical use. In sum, we present a generalizable method to screen for novel synergistic combinations, to identify particular mechanisms resulting in synergy, and to use the mechanistic knowledge to rationally design new combinations that bypass drug resistance.

High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance

PubMed Central

Lewis, Adam J.; Mulvey, Matthew A.

2017-01-01

Antibiotic-resistant infections kill approximately 23,000 people and cost $20,000,000,000 each year in the United States alone despite the widespread use of small-molecule antimicrobial combination therapy. Antibiotic combinations typically have an additive effect: the efficacy of the combination matches the sum of the efficacies of each antibiotic when used alone. Small molecules can also act synergistically when the efficacy of the combination is greater than the additive efficacy. However, synergistic combinations are rare and have been historically difficult to identify. High-throughput identification of synergistic pairs is limited by the scale of potential combinations: a modest collection of 1,000 small molecules involves 1 million pairwise combinations. Here, we describe a high-throughput method for rapid identification of synergistic small-molecule pairs, the overlap2 method (O2M). O2M extracts patterns from chemical-genetic datasets, which are created when a collection of mutants is grown in the presence of hundreds of different small molecules, producing a precise set of phenotypes induced by each small molecule across the mutant set. The identification of mutants that show the same phenotype when treated with known synergistic molecules allows us to pinpoint additional molecule combinations that also act synergistically. As a proof of concept, we focus on combinations with the antibiotics trimethoprim and sulfamethizole, which had been standard treatment against urinary tract infections until widespread resistance decreased efficacy. Using O2M, we screened a library of 2,000 small molecules and identified several that synergize with the antibiotic trimethoprim and/or sulfamethizole. The most potent of these synergistic interactions is with the antiviral drug azidothymidine (AZT). We then demonstrate that understanding the molecular mechanism underlying small-molecule synergistic interactions allows the rational design of additional combinations that bypass drug resistance. Trimethoprim and sulfamethizole are both folate biosynthesis inhibitors. We find that this activity disrupts nucleotide homeostasis, which blocks DNA replication in the presence of AZT. Building on these data, we show that other small molecules that disrupt nucleotide homeostasis through other mechanisms (hydroxyurea and floxuridine) also act synergistically with AZT. These novel combinations inhibit the growth and virulence of trimethoprim-resistant clinical Escherichia coli and Klebsiella pneumoniae isolates, suggesting that they may be able to be rapidly advanced into clinical use. In sum, we present a generalizable method to screen for novel synergistic combinations, to identify particular mechanisms resulting in synergy, and to use the mechanistic knowledge to rationally design new combinations that bypass drug resistance. PMID:28632788

X-ray characterization of solid small molecule organic materials

DOEpatents

Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

2014-06-10

The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

Group specific internal standard technology (GSIST) for simultaneous identification and quantification of small molecules

DOEpatents

Adamec, Jiri; Yang, Wen-Chu; Regnier, Fred E

2014-01-14

Reagents and methods are provided that permit simultaneous analysis of multiple diverse small molecule analytes present in a complex mixture. Samples are labeled with chemically identical but isotopically distince forms of the labeling reagent, and analyzed using mass spectrometry. A single reagent simultaneously derivatizes multiple small molecule analytes having different reactive functional groups.

Crossing borders to bind proteins--a new concept in protein recognition based on the conjugation of small organic molecules or short peptides to polypeptides from a designed set.

PubMed

Baltzer, Lars

2011-06-01

A new concept for protein recognition and binding is highlighted. The conjugation of small organic molecules or short peptides to polypeptides from a designed set provides binder molecules that bind proteins with high affinities, and with selectivities that are equal to those of antibodies. The small organic molecules or peptides need to bind the protein targets but only with modest affinities and selectivities, because conjugation to the polypeptides results in molecules with dramatically improved binder performance. The polypeptides are selected from a set of only sixteen sequences designed to bind, in principle, any protein. The small number of polypeptides used to prepare high-affinity binders contrasts sharply with the huge libraries used in binder technologies based on selection or immunization. Also, unlike antibodies and engineered proteins, the polypeptides have unordered three-dimensional structures and adapt to the proteins to which they bind. Binder molecules for the C-reactive protein, human carbonic anhydrase II, acetylcholine esterase, thymidine kinase 1, phosphorylated proteins, the D-dimer, and a number of antibodies are used as examples to demonstrate that affinities are achieved that are higher than those of the small molecules or peptides by as much as four orders of magnitude. Evaluation by pull-down experiments and ELISA-based tests in human serum show selectivities to be equal to those of antibodies. Small organic molecules and peptides are readily available from pools of endogenous ligands, enzyme substrates, inhibitors or products, from screened small molecule libraries, from phage display, and from mRNA display. The technology is an alternative to established binder concepts for applications in drug development, diagnostics, medical imaging, and protein separation.

Membrane Fusion Induced by Small Molecules and Ions

PubMed Central

Mondal Roy, Sutapa; Sarkar, Munna

2011-01-01

Membrane fusion is a key event in many biological processes. These processes are controlled by various fusogenic agents of which proteins and peptides from the principal group. The fusion process is characterized by three major steps, namely, inter membrane contact, lipid mixing forming the intermediate step, pore opening and finally mixing of inner contents of the cells/vesicles. These steps are governed by energy barriers, which need to be overcome to complete fusion. Structural reorganization of big molecules like proteins/peptides, supplies the required driving force to overcome the energy barrier of the different intermediate steps. Small molecules/ions do not share this advantage. Hence fusion induced by small molecules/ions is expected to be different from that induced by proteins/peptides. Although several reviews exist on membrane fusion, no recent review is devoted solely to small moleculs/ions induced membrane fusion. Here we intend to present, how a variety of small molecules/ions act as independent fusogens. The detailed mechanism of some are well understood but for many it is still an unanswered question. Clearer understanding of how a particular small molecule can control fusion will open up a vista to use these moleucles instead of proteins/peptides to induce fusion both in vivo and in vitro fusion processes. PMID:21660306

Perylene-Diimide Based Donor-Acceptor-Donor Type Small-Molecule Acceptors for Solution-Processable Organic Solar Cells

NASA Astrophysics Data System (ADS)

Ganesamoorthy, Ramasamy; Vijayaraghavan, Rajagopalan; Sakthivel, Pachagounder

2017-12-01

Development of nonfullerene acceptors plays an important role in the commercial availability of plastic solar cells. We report herein synthesis of bay-substituted donor-acceptor-donor (D-A-D)-type perylene diimide (PDI)-based small molecules (SM-1 to SM-4) by Suzuki coupling method and their use as acceptors in bulk heterojunction organic solar cells (BHJ-OSCs) with poly(3-hexylthiophene) (P3HT) polymer donor. We varied the number of electron-rich thiophene units and the solubilizing side chains and also evaluated the optical and electrochemical properties of the small molecules. The synthesized small molecules were confirmed by Fourier-transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and high-resolution mass spectroscopy (HR-MS). The small molecules showed extensive and strong absorption in the ultraviolet-visible (UV-Vis) region up to 750 nm, with bandgap (E_{{g}}^{{opt}} ) reduced below <2 eV. The energy levels of small molecules SM-1 to SM-4 were suitable for use as electron-accepting materials. The small molecules showed good thermal stability up to 300°C. BHJ-OSCs with SM-1 and P3HT polymer donor showed maximum power conversion efficiency (PCE) of 0.19% with V oc of 0.30 V, J sc of 1.72 mA cm-2, and fill factor (FF) of 37%. The PCE decreased with the number of thiophene units. The PCE of SM-2 was lower than that of SM-1. This difference in PCE can be explained by the higher aggregation tendency of the bithiophene compared with the thiophene unit. Introduction of the solubilizing group in the bay position increased the aggregation property, leading to much lower PCE than for the small molecules without solubilizing group.

Hierarchical virtual screening approaches in small molecule drug discovery.

PubMed

Kumar, Ashutosh; Zhang, Kam Y J

2015-01-01

Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

Confinement of water molecule inside (2, 2) graphyne nanotube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deb, Jyotirmoy; Bhattacharya, Barnali; Sarkar, Utpal, E-mail: utpalchemiitkgp@yahoo.com

2016-05-23

Using density functional theory (DFT) calculations with generalized gradient approximation, the interaction between H{sub 2}O molecule and (2, 2) graphyne nanotube (GNT) has been investigated. The stable configuration due to the insertion of H{sub 2}O molecule inside (2, 2) GNT is determined on the basis of binding energy. The band gap of the GNT decreases due to the confinement of H{sub 2}O molecule. The charge analysis reveals that electrons are shifted from the H{sub 2}O molecule to the GNT. The electronic property of the GNT is highly influenced by the presence of H{sub 2}O molecule; thus, we may design amore » GNT based sensor for the detection of water molecule.« less

Synthesis of Conjugated Small Molecules and Polymers by a Palladium Catalyzed Cyclopentannulation Strategy: Towards New Organic Semiconductors

NASA Astrophysics Data System (ADS)

Bheemireddy, Sambasiva Reddy

The utility of conjugated small molecules and polymers as organic semiconductors have seen a tremendous growth in research and development in academia as well as industry because of their processability and flexibility advantages in comparison to inorganic semiconductors. The extensive research over the years has produced a large number of p-type (hole conducting) and n-type (electron conducting) semiconductors that can be used to construct organic electronic devices. Of these materials, p-type semiconductors are more established and extensively studied because of the ease of preparation as well as their better general stability in comparison to n-type materials. Despite recent research into the development of n-type materials, fullerene (C60 and C 70) and its derivatives are still the predominant materials used as electron acceptors for OPV applications. By taking advantage of the electron accepting behavior of cyclopenta[hi]aceanthrylene fragment of C70, we have designed and synthesized new materials based on cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs). By using a newly developed palladium catalyzed cyclopentannulation methodology, 1,2,6,7- tetraarylcyclopenta[hi]aceanthrylenes were prepared by treating diarylethynylenes with 9,10-dibromoanthracene. Scholl cyclodehydrogenation was used to close the externally fused aryl groups to provide access to contorted 2,7,13,18- tetraalkoxytetrabenzo[f,h,r,t]rubicenes. The contortion provides access to more soluble materials than their planar counterparts but still ii allows significant pi-pi stacking between molecules. Using a modified palladium catalyzed cyclopentannulation polymerization followed by a cyclodehydrogenation reaction, a nonconventional synthesis of CP-PAH embedded ladder polymers was also achieved. These ladder polymers possess broad UV-Vis absorptions and narrow optical gaps of 1.17-1.29 eV. The synthesis of new donor-acceptor copolymers incorporating electron accepting 1,2,6,7- tetra(4-dodecylphenyl)dicyclopenta[cd,jk]pyrene was also achieved. The donor unit was varied between thiophene, bithiophene, and 1,4-diethynyl-2,5-bis((2-octyldodecyl)oxy)-benzene producing polymers with high molecular weights and considerably low band gaps. This newly developed cyclopentannulation method was also used to synthesize a new class of stabilized pentacene derivatives with externally fused five-membered rings. The target compounds were synthesized via chemical manipulation of a partially saturated 6,13-dibromopentacene precursor that can be fully aromatized in a final step via a DDQ mediated dehydrogenation reaction. Photodegradation studies reveal the new 1,2,8,9-tetraphenyldicyclopenta[fg,qr]pentacene derivatives are more photostable than TIPS-pentacene, and possess narrow optical gaps of 1.2 eV. Because anthradithophene (ADT) is more stable than pentacene while maintaining good electronic properties, the synthesis of cyclopentannulated anthradithiophenes (CP-ADTs) was also explored. Synthesis of a highly contorted ADT analogue was achieved by treating 5,11-dibromo-anthradithiophene with 3,3'-dimethoxy,1,1'-diphenyl acetylene under palladium catalyzed cyclopentannulation conditions followed by Scholl cyclodehydrogenation.

Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer's disease.

PubMed

Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R; Challa, Pavan Kumar; Cohen, Samuel I A; Linse, Sara; Dobson, Christopher M; Knowles, Tuomas P J; Vendruscolo, Michele

2017-01-10

The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer's disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery.

Synthesis of many different types of organic small molecules using one automated process.

PubMed

Li, Junqi; Ballmer, Steven G; Gillis, Eric P; Fujii, Seiko; Schmidt, Michael J; Palazzolo, Andrea M E; Lehmann, Jonathan W; Morehouse, Greg F; Burke, Martin D

2015-03-13

Small-molecule synthesis usually relies on procedures that are highly customized for each target. A broadly applicable automated process could greatly increase the accessibility of this class of compounds to enable investigations of their practical potential. Here we report the synthesis of 14 distinct classes of small molecules using the same fully automated process. This was achieved by strategically expanding the scope of a building block-based synthesis platform to include even C(sp3)-rich polycyclic natural product frameworks and discovering a catch-and-release chromatographic purification protocol applicable to all of the corresponding intermediates. With thousands of compatible building blocks already commercially available, many small molecules are now accessible with this platform. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis. Copyright © 2015, American Association for the Advancement of Science.

Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches.

PubMed

Rossetti, Marianna; Ippodrino, Rudy; Marini, Bruna; Palleschi, Giuseppe; Porchetta, Alessandro

2018-06-13

The development of rapid, cost-effective, and single-step methods for the detection of small molecules is crucial for improving the quality and efficiency of many applications ranging from life science to environmental analysis. Unfortunately, current methodologies still require multiple complex, time-consuming washing and incubation steps, which limit their applicability. In this work we present a competitive DNA-based platform that makes use of both programmable DNA-switches and antibodies to detect small target molecules. The strategy exploits both the advantages of proximity-based methods and structure-switching DNA-probes. The platform is modular and versatile and it can potentially be applied for the detection of any small target molecule that can be conjugated to a nucleic acid sequence. Here the rational design of programmable DNA-switches is discussed, and the sensitive, rapid, and single-step detection of different environmentally relevant small target molecules is demonstrated.

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

DOE PAGES

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.; ...

2016-08-30

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

Small Molecule Signaling Agents: The Integrated Chemistry and Biochemistry of Nitrogen Oxides, Oxides of Carbon, Dioxygen, Hydrogen Sulfide, and Their Derived Species

PubMed Central

Fukuto, Jon M.; Carrington, Samantha J.; Tantillo, Dean J.; Harrison, Jason G.; Ignarro, Louis J.; Freeman, Bruce A.; Chen, Andrew; Wink, David A.

2014-01-01

Several small molecule species formally known primarily as toxic gases have, over the past 20 years, been shown to be endogenously generated signaling molecules. The biological signaling associated with the small molecules NO, CO, H2S (and the nonendogenously generated O2), and their derived species have become a topic of extreme interest. It has become increasingly clear that these small molecule signaling agents form an integrated signaling web that affects/regulates numerous physiological processes. The chemical interactions between these species and each other or biological targets is an important factor in their roles as signaling agents. Thus, a fundamental understanding of the chemistry of these molecules is essential to understanding their biological/physiological utility. This review focuses on this chemistry and attempts to establish the chemical basis for their signaling functions. PMID:22263838

Fluorination-enabled optimal morphology leads to over 11% efficiency for inverted small-molecule organic solar cells

PubMed Central

Deng, Dan; Zhang, Yajie; Zhang, Jianqi; Wang, Zaiyu; Zhu, Lingyun; Fang, Jin; Xia, Benzheng; Wang, Zhen; Lu, Kun; Ma, Wei; Wei, Zhixiang

2016-01-01

Solution-processable small molecules for organic solar cells have attracted intense attention for their advantages of definite molecular structures compared with their polymer counterparts. However, the device efficiencies based on small molecules are still lower than those of polymers, especially for inverted devices, the highest efficiency of which is <9%. Here we report three novel solution-processable small molecules, which contain π-bridges with gradient-decreased electron density and end acceptors substituted with various fluorine atoms (0F, 1F and 2F, respectively). Fluorination leads to an optimal active layer morphology, including an enhanced domain purity, the formation of hierarchical domain size and a directional vertical phase gradation. The optimal morphology balances charge separation and transfer, and facilitates charge collection. As a consequence, fluorinated molecules exhibit excellent inverted device performance, and an average power conversion efficiency of 11.08% is achieved for a two-fluorine atom substituted molecule. PMID:27991486

High-order oligomers of intrinsically disordered brain proteins BASP1 and GAP-43 preserve the structural disorder.

PubMed

Forsova, Oksana S; Zakharov, Vladislav V

2016-04-01

Brain acid-soluble protein-1 (BASP1) and growth-associated protein-43 (GAP-43) are presynaptic membrane proteins participating in axon guidance, neuroregeneration and synaptic plasticity. They are presumed to sequester phosphatidylinositol-4,5-bisphosphate (PIP2 ) in lipid rafts. Previously we have shown that the proteins form heterogeneously sized oligomers in the presence of anionic phospholipids or SDS at submicellar concentration. BASP1 and GAP-43 are intrinsically disordered proteins (IDPs). In light of this, we investigated the structure of their oligomers. Using partial cross-linking of the oligomers with glutaraldehyde, the aggregation numbers of BASP1 and GAP-43 were estimated as 10-14 and 6-7 monomer subunits, respectively. The cross-linking pattern indicated that the subunits are circularly arranged. The circular dichroism (CD) spectra of the monomers were characteristic of coil-like IDPs showing unordered structure with a high population of polyproline-II conformation. The oligomerization was accompanied by a minor CD spectral change attributable to formation of a small amount of α-helix. The number of residues in the α-helical conformation was estimated as 13 in BASP1 and 18 in GAP-43. However, the overall structure of the oligomers remained disordered, indicating a high degree of 'fuzziness'. This was confirmed by measuring the hydrodynamic dimensions of the oligomers using polyacrylamide gradient gel electrophoresis and size-exclusion chromatography, and by assaying their sensitivity to proteolytic digestion. There is evidence that the observed α-helical folding occurs within the basic effector domains, which are presumably tethered together via anionic molecules of SDS or PIP2 . We conclude that BASP1 and GAP-43 oligomers preserve a mostly disordered structure, which may be of great importance for their function in PIP2 signaling pathway. © 2016 Federation of European Biochemical Societies.

[Effect of annealing temperature on the crystallization and spectroscopic response of a small-molecule semiconductor doped in polymer film].

PubMed

Yin, Ming; Zhang, Xin-Ping; Liu, Hong-Mei

2012-11-01

The crystallization properties of the perylene (EPPTC) molecules doped in the solid film of the derivative of polyfluorene (F8BT) at different annealing temperatures, as well as the consequently induced spectroscopic response of the exciplex emission in the heterojunction structures, were studied in the present paper. Experimental results showed that the phase separation between the small and the polymer molecules in the blend film is enhanced with increasing the annealing temperature, which leads to the crystallization of the EPPTC molecules due to the strong pi-pi stacking. The size of the crystal phase increases with increasing the annealing temperature. However, this process weakens the mechanisms of the heterojunction configuration, thus, the total interfacial area between the small and the polymer molecules and the amount of exciplex are reduced significantly in the blend film. Meanwhile, the energy transfer from the polymer to the small molecules is also reduced. As a result, the emission from the exciplex becomes weaker with increasing the annealing temperature, whereas the stronger emission from the polymer molecules and from the crystal phase of the small molecules can be observed. These experimental results are very important for understanding and tailoring the organic heterojunction structures. Furthermore, this provides photophysics for improving the performance of photovoltaic or solar cell devices.

Tandem array of nanoelectronic readers embedded coplanar to a fluidic nanochannel for correlated single biopolymer analysis

PubMed Central

Lesser-Rojas, Leonardo; Sriram, K. K.; Liao, Kuo-Tang; Lai, Shui-Chin; Kuo, Pai-Chia; Chu, Ming-Lee; Chou, Chia-Fu

2014-01-01

We have developed a two-step electron-beam lithography process to fabricate a tandem array of three pairs of tip-like gold nanoelectronic detectors with electrode gap size as small as 9 nm, embedded in a coplanar fashion to 60 nm deep, 100 nm wide, and up to 150 μm long nanochannels coupled to a world-micro-nanofluidic interface for easy sample introduction. Experimental tests with a sealed device using DNA-protein complexes demonstrate the coplanarity of the nanoelectrodes to the nanochannel surface. Further, this device could improve transverse current detection by correlated time-of-flight measurements of translocating samples, and serve as an autocalibrated velocimeter and nanoscale tandem Coulter counters for single molecule analysis of heterogeneous samples. PMID:24753731

Next-Generation Connexin and Pannexin Cell Biology.

PubMed

Esseltine, Jessica L; Laird, Dale W

2016-12-01

Connexins and pannexins are two families of large-pore channel forming proteins that are capable of passing small signaling molecules. While connexins serve the seminal task of direct gap junctional intercellular communication, pannexins are far less understood but function primarily as single membrane channels in autocrine and paracrine signaling. Advancements in connexin and pannexin biology in recent years has revealed that in addition to well-described classical functions at the plasma membrane, exciting new evidence suggests that connexins and pannexins participate in alternative pathways involving multiple intracellular compartments. Here we briefly highlight classical functions of connexins and pannexins but focus our attention mostly on the transformative findings that suggest that these channel-forming proteins may serve roles far beyond our current understandings. Copyright © 2016 Elsevier Ltd. All rights reserved.

Innovation in academic chemical screening: filling the gaps in chemical biology.

PubMed

Hasson, Samuel A; Inglese, James

2013-06-01

Academic screening centers across the world have endeavored to discover small molecules that can modulate biological systems. To increase the reach of functional-genomic and chemical screening programs, universities, research institutes, and governments have followed their industrial counterparts in adopting high-throughput paradigms. As academic screening efforts have steadily grown in scope and complexity, so have the ideas of what is possible with the union of technology and biology. This review addresses the recent conceptual and technological innovation that has been propelling academic screening into its own unique niche. In particular, high-content and whole-organism screening are changing how academics search for novel bioactive compounds. Importantly, we recognize examples of successful chemical probe development that have punctuated the changing technology landscape. Published by Elsevier Ltd.

Hippocampal and cortical neuronal growth mediated by the small molecule natural product clovanemagnolol.

PubMed

Khaing, Zin; Kang, Danby; Camelio, Andrew M; Schmidt, Christine E; Siegel, Dionicio

2011-08-15

The use of small molecule surrogates of growth factors that directly or indirectly promote growth represents an attractive approach to regenerative medicine. With synthetic access to clovanemagnolol, a small molecule initially isolated from the bark of the Bigleaf Magnolia tree, we have examined the small molecule's ability to promote growth of embryonic hippocampal and cortical neurons in serum-free medium. Comparisons with magnolol, a known promoter of growth, reveals that clovanmagnolol is a potent neurotrophic agent, promoting neuronal growth at concentrations of 10 nM. In addition, both clovanemagnolol and magnolol promote growth through a biphasic dose response. Copyright © 2011 Elsevier Ltd. All rights reserved.

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

PubMed

Usanov, Dmitry L; Chan, Alix I; Maianti, Juan Pablo; Liu, David R

2018-07-01

DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC 50  = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery.

Use of mRNA expression signatures to discover small molecule inhibitors of skeletal muscle atrophy

PubMed Central

Adams, Christopher M.; Ebert, Scott M.; Dyle, Michael C.

2017-01-01

Purpose of review Here, we discuss a recently developed experimental strategy for discovering small molecules with potential to prevent and treat skeletal muscle atrophy. Recent findings Muscle atrophy involves and requires widespread changes in skeletal muscle gene expression, which generate complex but measurable patterns of positive and negative changes in skeletal muscle mRNA levels (a.k.a. mRNA expression signatures of muscle atrophy). Many bioactive small molecules generate their own characteristic mRNA expression signatures, and by identifying small molecules whose signatures approximate mirror images of muscle atrophy signatures, one may identify small molecules with potential to prevent and/or reverse muscle atrophy. Unlike a conventional drug discovery approach, this strategy does not rely on a predefined molecular target but rather exploits the complexity of muscle atrophy to identify small molecules that counter the entire spectrum of pathological changes in atrophic muscle. We discuss how this strategy has been used to identify two natural compounds, ursolic acid and tomatidine, that reduce muscle atrophy and improve skeletal muscle function. Summary Discovery strategies based on mRNA expression signatures can elucidate new approaches for preserving and restoring muscle mass and function. PMID:25807353

Use of mRNA expression signatures to discover small molecule inhibitors of skeletal muscle atrophy.

PubMed

Adams, Christopher M; Ebert, Scott M; Dyle, Michael C

2015-05-01

Here, we discuss a recently developed experimental strategy for discovering small molecules with potential to prevent and treat skeletal muscle atrophy. Muscle atrophy involves and requires widespread changes in skeletal muscle gene expression, which generate complex but measurable patterns of positive and negative changes in skeletal muscle mRNA levels (a.k.a. mRNA expression signatures of muscle atrophy). Many bioactive small molecules generate their own characteristic mRNA expression signatures, and by identifying small molecules whose signatures approximate mirror images of muscle atrophy signatures, one may identify small molecules with potential to prevent and/or reverse muscle atrophy. Unlike a conventional drug discovery approach, this strategy does not rely on a predefined molecular target but rather exploits the complexity of muscle atrophy to identify small molecules that counter the entire spectrum of pathological changes in atrophic muscle. We discuss how this strategy has been used to identify two natural compounds, ursolic acid and tomatidine, that reduce muscle atrophy and improve skeletal muscle function. Discovery strategies based on mRNA expression signatures can elucidate new approaches for preserving and restoring muscle mass and function.

Mass amplifying probe for sensitive fluorescence anisotropy detection of small molecules in complex biological samples.

PubMed

Cui, Liang; Zou, Yuan; Lin, Ninghang; Zhu, Zhi; Jenkins, Gareth; Yang, Chaoyong James

2012-07-03

Fluorescence anisotropy (FA) is a reliable and excellent choice for fluorescence sensing. One of the key factors influencing the FA value for any molecule is the molar mass of the molecule being measured. As a result, the FA method with functional nucleic acid aptamers has been limited to macromolecules such as proteins and is generally not applicable for the analysis of small molecules because their molecular masses are relatively too small to produce observable FA value changes. We report here a molecular mass amplifying strategy to construct anisotropy aptamer probes for small molecules. The probe is designed in such a way that only when a target molecule binds to the probe does it activate its binding ability to an anisotropy amplifier (a high molecular mass molecule such as protein), thus significantly increasing the molecular mass and FA value of the probe/target complex. Specifically, a mass amplifying probe (MAP) consists of a targeting aptamer domain against a target molecule and molecular mass amplifying aptamer domain for the amplifier protein. The probe is initially rendered inactive by a small blocking strand partially complementary to both target aptamer and amplifier protein aptamer so that the mass amplifying aptamer domain would not bind to the amplifier protein unless the probe has been activated by the target. In this way, we prepared two probes that constitute a target (ATP and cocaine respectively) aptamer, a thrombin (as the mass amplifier) aptamer, and a fluorophore. Both probes worked well against their corresponding small molecule targets, and the detection limits for ATP and cocaine were 0.5 μM and 0.8 μM, respectively. More importantly, because FA is less affected by environmental interferences, ATP in cell media and cocaine in urine were directly detected without any tedious sample pretreatment. Our results established that our molecular mass amplifying strategy can be used to design aptamer probes for rapid, sensitive, and selective detection of small molecules by means of FA in complex biological samples.

Low Band Gap Thiophene-Perylene Diimide Systems with Tunable Charge Transport Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balaji, Ganapathy; Kale, Tejaswini S.; Keerthi, Ashok

2011-01-07

Perylenediimide-pentathiophene systems with varied architecture of thiophene units were synthesized. The photophysical, electrochemical, and charge transport behavior of the synthesized compounds were studied. Both molecules showed a low band gap of ~1.4 eV. Surprisingly, the molecule with pentathiophene attached via β-position to the PDI unit upon annealing showed a predominant hole mobility of 1 × 10 -4 cm 2 V -1 s -1 whereas the compound with branched pentathiophene attached via β-position showed an electron mobility of 9.8 × 10 -7 cm 2 V -1 s -1. This suggests that charge transport properties can be tuned by simply varying themore » architecture of pentathiophene units.« less

Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering

PubMed Central

Feng, Simin; dos Santos, Maria Cristina; Carvalho, Bruno R.; Lv, Ruitao; Li, Qing; Fujisawa, Kazunori; Elías, Ana Laura; Lei, Yu; Perea-López, Nestor; Endo, Morinobu; Pan, Minghu; Pimenta, Marcos A.; Terrones, Mauricio

2016-01-01

As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (EF) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule’s vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10−11 M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps. PMID:27532043

Influence of thermocleavable functionality on organic field-effect transistor performance of small molecules

NASA Astrophysics Data System (ADS)

Mahale, Rajashree Y.; Dharmapurikar, Satej S.; Chini, Mrinmoy Kumar; Venugopalan, Vijay

2017-06-01

Diketopyrrolopyrrole based donor-acceptor-donor conjugated small molecules using ethylene dioxythiophene as a donor was synthesized. Electron deficient diketopyrrolopyrrole unit was substituted with thermocleavable (tert-butyl acetate) side chains. The thermal treatment of the molecules at 160 °C eliminated the tert-butyl ester group results in the formation of corresponding acid. Optical and theoretical studies revealed that the molecules adopted a change in molecular arrangement after thermolysis. The conjugated small molecules possessed p-channel charge transport characteristics in organic field effect transistors. The charge carrier mobility was increased after thermolysis of tert-butyl ester group to 5.07 × 10-5 cm2/V s.

Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1

PubMed Central

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; Ramanathan, Arvind; Zhang, Weixing; Shelat, Anang A.; Zuo, Jian; Kriwacki, Richard W.

2015-01-01

Disordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27Kip1 (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A). PMID:26507530

Discovery of Small Molecules that Inhibit the Disordered Protein, p27 Kip1

DOE PAGES

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; ...

2015-10-28

In disordered proteins we see that they are highly prevalent in biological systems. They control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27 Kip1 (p27). Moreover, two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groupsmore » of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule: disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of- principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).« less

Atf3 mutant mice show reduced axon regeneration and impaired regeneration-associated gene induction after peripheral nerve injury

PubMed Central

Gey, Manuel; Wanner, Renate; Schilling, Corinna; Pedro, Maria T.; Sinske, Daniela

2016-01-01

Axon injury in the peripheral nervous system (PNS) induces a regeneration-associated gene (RAG) response. Atf3 (activating transcription factor 3) is such a RAG and ATF3's transcriptional activity might induce ‘effector’ RAGs (e.g. small proline rich protein 1a (Sprr1a), Galanin (Gal), growth-associated protein 43 (Gap43)) facilitating peripheral axon regeneration. We provide a first analysis of Atf3 mouse mutants in peripheral nerve regeneration. In Atf3 mutant mice, facial nerve regeneration and neurite outgrowth of adult ATF3-deficient primary dorsal root ganglia neurons was decreased. Using genome-wide transcriptomics, we identified a neuropeptide-encoding RAG cluster (vasoactive intestinal peptide (Vip), Ngf, Grp, Gal, Pacap) regulated by ATF3. Exogenous administration of neuropeptides enhanced neurite growth of Atf3 mutant mice suggesting that these molecules might be effector RAGs of ATF3's pro-regenerative function. In addition to the induction of growth-promoting molecules, we present data that ATF3 suppresses growth-inhibiting molecules such as chemokine (C-C motif) ligand 2. In summary, we show a pro-regenerative ATF3 function during PNS nerve regeneration involving transcriptional activation of a neuropeptide-encoding RAG cluster. ATF3 is a general injury-inducible factor, therefore ATF3-mediated mechanisms identified herein might apply to other cell and injury types. PMID:27581653

Simultaneous protection of organic p- and n-channels in complementary inverter from aging and bias-stress by DNA-base guanine/Al2O3 double layer.

PubMed

Lee, Junyeong; Hwang, Hyuncheol; Min, Sung-Wook; Shin, Jae Min; Kim, Jin Sung; Jeon, Pyo Jin; Lee, Hee Sung; Im, Seongil

2015-01-28

Although organic field-effect transistors (OFETs) have various advantages of lightweight, low-cost, mechanical flexibility, and nowadays even higher mobility than amorphous Si-based FET, stability issue under bias and ambient condition critically hinder its practical application. One of the most detrimental effects on organic layer comes from penetrated atmospheric species such as oxygen and water. To solve such degradation problems, several molecular engineering tactics are introduced: forming a kinetic barrier, lowering the level of molecule orbitals, and increasing the band gap. However, direct passivation of organic channels, the most promising strategy, has not been reported as often as other methods. Here, we resolved the ambient stability issues of p-type (heptazole)/or n-type (PTCDI-C13) OFETs and their bias-stability issues at once, using DNA-base small molecule guanine (C5H5N5O)/Al2O3 bilayer. The guanine protects the organic channels as buffer/and H getter layer between the channels and capping Al2O3, whereas the oxide capping resists ambient molecules. As a result, both p-type and n-type OFETs are simultaneously protected from gate-bias stress and 30 days-long ambient aging, finally demonstrating a highly stable, high-gain complementary-type logic inverter.

Strategy to discover diverse optimal molecules in the small molecule universe.

PubMed

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

PubMed Central

2015-01-01

The small molecule universe (SMU) is defined as a set of over 1060 synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc.2013, 135, 7296–730323548177) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 105 molecules. PMID:25594586

Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains.

PubMed

Bulashevska, Alla; Stein, Martin; Jackson, David; Eils, Roland

2009-12-01

Accurate computational methods that can help to predict biological function of a protein from its sequence are of great interest to research biologists and pharmaceutical companies. One approach to assume the function of proteins is to predict the interactions between proteins and other molecules. In this work, we propose a machine learning method that uses a primary sequence of a domain to predict its propensity for interaction with small molecules. By curating the Pfam database with respect to the small molecule binding ability of its component domains, we have constructed a dataset of small molecule binding and non-binding domains. This dataset was then used as training set to learn a Bayesian classifier, which should distinguish members of each class. The domain sequences of both classes are modelled with Markov chains. In a Jack-knife test, our classification procedure achieved the predictive accuracies of 77.2% and 66.7% for binding and non-binding classes respectively. We demonstrate the applicability of our classifier by using it to identify previously unknown small molecule binding domains. Our predictions are available as supplementary material and can provide very useful information to drug discovery specialists. Given the ubiquitous and essential role small molecules play in biological processes, our method is important for identifying pharmaceutically relevant components of complete proteomes. The software is available from the author upon request.

Small Molecule Protection of Bone Marrow Hematopoietic Stem Cells

DTIC Science & Technology

2015-10-01

several recently identified small molecules can protect hematopoietic stem cells (HSCs) from damage or killing by endogenous aldehydes . Proof-of-concept...anemia bone marrow failure CD34+ hematopoietic stem cells aldehydes formaldehyde DNA damage DNA base adduct DNA-protein crosslink mass...below. Revised Specific Aim 1: Small molecule protection of human cells from aldehyde - induced killing (in vitro studies - no mice or human subjects

Integrating Sub-3 nm Plasmonic Gaps into Solid-State Nanopores.

PubMed

Shi, Xin; Verschueren, Daniel; Pud, Sergii; Dekker, Cees

2018-05-01

Plasmonic nanopores combine the advantages of nanopore sensing and surface plasmon resonances by introducing confined electromagnetic fields to a solid-state nanopore. Ultrasmall nanogaps between metallic nanoantennas can generate the extremely enhanced localized electromagnetic fields necessary for single-molecule optical sensing and manipulation. Challenges in fabrication, however, hamper the integration of such nanogaps into nanopores. Here, a top-down approach for integrating a plasmonic antenna with an ultrasmall nanogap into a solid-state nanopore is reported. Employing a two-step e-beam lithography process, the reproducible fabrication of nanogaps down to a sub-1 nm scale is demonstrated. Subsequently, nanopores are drilled through the 20 nm SiN membrane at the center of the nanogap using focused-electron-beam sculpting with a transmission electron microscope, at the expense of a slight gap expansion for the smallest gaps. Using this approach, sub-3 nm nanogaps can be readily fabricated on solid-state nanopores. The functionality of these plasmonic nanopores for single-molecule detection is shown by performing DNA translocations. These integrated devices can generate intense electromagnetic fields at the entrance of the nanopore and can be expected to find applications in nanopore-based single-molecule trapping and optical sensing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical and electronic properties of SO2 molecule adsorbed on Si-doped (8, 0) boron nitride nanotube

NASA Astrophysics Data System (ADS)

Guo, Shuang-Shuang; Wei, Xiu-Mei; Zhang, Jian-Min; Zhu, Gang-Qiang; Guo, Wan-Jin

2016-09-01

The study of the optical properties of pristine BNNT, Si-doped BNNTs and SO2 molecule adsorption on Si-doped BNNTs is that, to our knowledge, few relevant research have ever been found. In this paper, the adsorption behaviors of Sulfur dioxide (SO2) molecule on Si-doped Boron nitride nanotubes (BNNTs) are investigated applying the first-principles calculations. The main contribution of this paper is that the foremost investigation for the optical properties of the pristine BNNT, Si-doped BNNTs and SO2 adsorption on Si-doped BNNTs. Additionally, the electronic properties and the structural properties are also presented. In our calculations of optical properties, the dielectric constant, the refractive index and the absorption coefficient are obtained. Comparing the pristine BNNT, our results indicate that, the blue-shifts (in the main peaks of the dielectric constant of SiB -BNNT and SO2-SiB -BNNT), and the red-shifts (in the main peaks of the refractive index of SiN -BNNT and SO2-SiN -BNNT) are appeared. Under these conditions, Si-doped BNNT and Si-doped BNNT with SO2 adsorption, the gaps are reduced both for the speculated optical band gaps and the electronic structure band gaps.

Star-Shaped Conjugated Molecules with Oxa- or Thiadiazole Bithiophene Side Arms.

PubMed

Kotwica, Kamil; Kostyuchenko, Anastasia S; Data, Przemyslaw; Marszalek, Tomasz; Skorka, Lukasz; Jaroch, Tomasz; Kacka, Sylwia; Zagorska, Malgorzata; Nowakowski, Robert; Monkman, Andrew P; Fisyuk, Alexander S; Pisula, Wojciech; Pron, Adam

2016-08-08

Star-shaped conjugated molecules, consisting of a benzene central unit symmetrically trisubstituted with either oxa- or thiadiazole bithiophene groups, were synthesized as promising molecules and building blocks for application in (opto)electronics and electrochromic devices. Their optical (Eg (opt)) as well as electrochemical (Eg (electro)) band gaps depended on the type of the side arm and the number of solubilizing alkyl substituents. Oxadiazole derivatives showed Eg (opt) slightly below 3 eV and by 0.2 eV larger than those determined for thiadiazole-based compounds. The presence of alkyl substituents in the arms additionally lowered the band gap. The obtained compounds were efficient electroluminophores in guest/host-type light-emitting diodes. They also showed a strong tendency to self-organize in monolayers deposited on graphite, as evidenced by scanning tunneling microscopy. The structural studies by X-ray scattering revealed the formation of supramolecular columnar stacks in which the molecules were organized. Differences in macroscopic alignment in the specimen indicated variations in the self-assembly mechanism between the molecules. The compounds as trifunctional monomers were electrochemically polymerized to yield the corresponding polymer network. As shown by UV/Vis-NIR spectroelectrochemical studies, these networks exhibited reversible electrochromic behavior both in the oxidation and in the reduction modes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nomenclature101.com: A Free, Student-Driven Organic Chemistry Nomenclature Learning Tool

ERIC Educational Resources Information Center

Flynn, Alison B.; Caron, Jeanette; Laroche, Jamey; Daviau-Duguay, Melissa; Marcoux, Caroline; Richard, Gise`le

2014-01-01

Fundamental to a student's understanding of organic chemistry is the ability to interpret and use its language, including molecules' names and other key terms. A learning gap exists in that students often struggle with organic nomenclature. Although many resources describe the rules for naming molecules, there is a paucity of resources…

DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.

PubMed

Lagorce, David; Pencheva, Tania; Villoutreix, Bruno O; Miteva, Maria A

2009-11-13

Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL).

PubMed

Melagraki, Georgia; Ntougkos, Evangelos; Rinotas, Vagelis; Papaneophytou, Christos; Leonis, Georgios; Mavromoustakos, Thomas; Kontopidis, George; Douni, Eleni; Afantitis, Antreas; Kollias, George

2017-04-01

We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos.insilicotox.com/TNFPubChem/. We thus generated a priority list of nine small molecules as candidates for direct TNF function inhibition. In vitro evaluation of these compounds led to the selection of two small molecules that act as potent direct inhibitors of TNF function, with IC50 values comparable to those of a previously-described direct inhibitor (SPD304), but with significantly reduced toxicity. These molecules were also identified as RANKL inhibitors and validated in vitro with respect to this second functionality. Direct binding of the two compounds was confirmed both for TNF and RANKL, as well as their ability to inhibit the biologically-active trimer forms. Molecular dynamics calculations were also carried out for the two small molecules in each protein to offer additional insight into the interactions that govern TNF and RANKL complex formation. To our knowledge, these compounds, namely T8 and T23, constitute the second and third published examples of dual small-molecule direct function inhibitors of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.

Lateral diffusion and signaling of receptor for advanced glycation end-products (RAGE): a receptor involved in chronic inflammation.

PubMed

Syed, Aleem; Zhu, Qiaochu; Smith, Emily A

2018-01-01

Membrane diffusion is one of the key mechanisms in the cellular function of receptors. The signaling of receptors for advanced glycation end-products (RAGE) has been extensively studied in the context of several pathological conditions, however, very little is known about RAGE diffusion. To fill this gap, RAGE lateral diffusion is probed in native, cholesterol-depleted, and cytoskeleton-altered cellular conditions. In native GM07373 cellular conditions, RAGE has a 90% mobile fraction and an average diffusion coefficient of 0.3 μm 2 /s. When depolymerization of the actin cytoskeleton is inhibited with the small molecule jasplakinolide (Jsp), the RAGE mobile fraction and diffusion coefficient decrease by 22 and 37%, respectively. In contrast, depolymerizing the filamentous actin cytoskeleton using the small molecule cytochalasin D (CD) does not alter the RAGE diffusion properties. There is a 70 and 50% decrease in phosphorylation of extracellular signal-regulated kinase (p-ERK) when the actin cytoskeleton is disrupted by CD or Jsp, respectively, in RAGE-expressing GM07373 cells. Disrupting the actin cytoskeleton in GM07373 cells that do not express detectable amounts of RAGE results in no change in p-ERK. Cholesterol depletion results in no statistically significant change in the diffusion properties of RAGE or p-ERK. This work presents a strong link between the actin cytoskeleton and RAGE diffusion and downstream signaling, and serves to further our understanding of the factors influencing RAGE lateral diffusion.

Probing the energetics of organic–nanoparticle interactions of ethanol on calcite

DOE PAGES

Wu, Di; Navrotsky, Alexandra

2015-04-13

Knowing the nature of interactions between small organic molecules and surfaces of nanoparticles (NP) is crucial for fundamental understanding of natural phenomena and engineering processes. In this paper, we report direct adsorption enthalpy measurement of ethanol on a series of calcite nanocrystals, with the aim of mimicking organic–NP interactions in various environments. The energetics suggests a spectrum of adsorption events as a function of coverage: strongest initial chemisorption on active sites on fresh calcite surfaces, followed by major chemical binding to form an ethanol monolayer and, subsequently, very weak, near-zero energy, physisorption. Furthermore, these thermochemical observations directly support a structuremore » where the ethanol monolayer is bonded to the calcite surface through its polar hydroxyl group, leaving the hydrophobic ends of the ethanol molecules to interact only weakly with the next layer of adsorbing ethanol and resulting in a spatial gap with low ethanol density between the monolayer and subsequent added ethanol molecules, as predicted by molecular dynamics and density functional calculations. Such an ordered assembly of ethanol on calcite NP is analogous to, although less strongly bonded than, a capping layer of organics intentionally introduced during NP synthesis, and suggests a continuous variation of surface structure depending on molecular chemistry, ranging from largely disordered surface layers to ordered layers that nevertheless are mobile and can rearrange or be displaced by other molecules to strongly bonded immobile organic capping layers. Finally, these differences in surface structure will affect chemical reactions, including the further nucleation and growth of nanocrystals on organic ligand-capped surfaces.« less

Saturn's Misbegotten Moonlets

NASA Astrophysics Data System (ADS)

Spitale, Joseph N.

2017-06-01

Saturn's rings are interspersed with numerous narrow (tens of km wide) gaps. Two of the largest of these gaps -- Encke and Keeler -- contain satellites -- Pan and Daphnis -- that maintain their respective gaps via the classical Goldreich/Tremaine-style shepherding mechanism wherein angular momentum is transferred across the essentially empty gap via torques acting between the satellites and the ring. Other prominent gaps are shepherded by resonances with external satellites or planetary modes: Mimas shepherds the outer edge of the B ring, clearing the inner part of the Cassini Division, Titan shepherds the Columbo ringlet / gap, and the Maxwell ringlet / gap is likely maintained by a resonance with a planetary mode. Prior to Cassini, it was expected that all of the gaps would be shepherded in a similar manner.However, many small gaps do not correspond with known resonances, and no satellites were spotted within those gaps during Cassini's prime and extended mission. To address this issue, a series of Cassini imaging observations were planned to examine 11 gaps in the C ring and Cassini division at a resolution and longitudinal coverage sufficient to either discover the shepherds or rule out their presence. The survey discovered no embedded satellites. Longitudinal coverage was incomplete, but within longitudes covered by the survey, satellites are ruled out to sizes in the 100-m range, far too small keep the observed gaps open. It is possible (about even odds) that there could be a larger satellite residing at a longitude not covered in the survey, but the probability that the survey was unfortunate enough to miss significant satellites in all 11 gaps is exceedingly small (~0.002%). Moreover, these gaps appear in earlier imaging sequences, with some high-resolution coverage, so the true probability is smaller yet. Therefore, a new theory is likely needed to explain the presence of the gaps.

Profiling protein function with small molecule microarrays

PubMed Central

Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

2002-01-01

The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

The effect of disorder of small spheres on the photonic properties of the inverse binary NaCl-like structure

NASA Astrophysics Data System (ADS)

Pattabhiraman, Harini; Dijkstra, Marjolein

2017-09-01

Inverse opal structures are experimentally realisable photonic band gap materials. They suffer from the drawback of possessing band gaps that are extremely susceptible to structural disorders. A binary colloidal NaCl lattice, which is also experimentally realisable, is a promising alternative to these opals. In this work, we systematically analyse the effect of structural disorder of the small spheres on the photonic properties of an inverse binary NaCl lattice with a size ratio of 0.30 between the small and large spheres. The types of structural disorders studied include the position of the small spheres in the octahedral void of the large spheres, polydispersity in size of the small spheres, and the fraction of small spheres in the crystal. We find a low susceptibility of the band gap of the inverse NaCl lattice to the disorder of the small spheres.

Free-standing few-layered graphene oxide films: selective, steady and lasting permeation of organic molecules with adjustable speeds

NASA Astrophysics Data System (ADS)

Huang, Tao; An, Qi; Luan, Xinglong; Zhang, Qian; Zhang, Yihe

2016-01-01

A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications.A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications. Electronic supplementary information (ESI) available: AFM images of GO and GO films, UV-vis spectra of delayed release, and permeation fidelities. See DOI: 10.1039/c5nr08129g

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease

PubMed Central

Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R.; Challa, Pavan Kumar; Cohen, Samuel I. A.; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

2017-01-01

The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer’s disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery. PMID:28011763

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reznik, Ed; Christodoulou, Dimitris; Goldford, Joshua E.

Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurementsmore » and the SMRN to make inferences on the sensitivity of enzymes to their regulators. By generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.« less

Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules

PubMed Central

Park, Hahnbeom; Bradley, Philip; Greisen, Per; Liu, Yuan; Mulligan, Vikram Khipple; Kim, David E.; Baker, David; DiMaio, Frank

2017-01-01

Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric structure prediction, protein-protein and protein-ligand docking, protein sequence design, and prediction of the free energy changes by mutation, while reasonably recapitulating small-molecule thermodynamic properties. PMID:27766851

Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations.

PubMed

Tran, Tuan; Disney, Matthew D

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here, we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (among a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole and pyridinium chemotypes allow for specific recognition of RNA motifs. As targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses.

Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10.

PubMed

Yang, Wang-Yong; Gao, Rui; Southern, Mark; Sarkar, Partha S; Disney, Matthew D

2016-06-01

RNA is an important target for chemical probes of function and lead therapeutics; however, it is difficult to target with small molecules. One approach to tackle this problem is to identify compounds that target RNA structures and utilize them to multivalently target RNA. Here we show that small molecules can be identified to selectively bind RNA base pairs by probing a library of RNA-focused small molecules. A small molecule that selectively binds AU base pairs informed design of a dimeric compound (2AU-2) that targets the pathogenic RNA, expanded r(AUUCU) repeats, that causes spinocerebellar ataxia type 10 (SCA10) in patient-derived cells. Indeed, 2AU-2 (50 nM) ameliorates various aspects of SCA10 pathology including improvement of mitochondrial dysfunction, reduced activation of caspase 3, and reduction of nuclear foci. These studies provide a first-in-class chemical probe to study SCA10 RNA toxicity and potentially define broadly applicable compounds targeting RNA AU base pairs in cells.

Identifying the Preferred RNA Motifs and Chemotypes that Interact by Probing Millions of Combinations

PubMed Central

Tran, Tuan; Disney, Matthew D.

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (amongst a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole, and pyridinium chemotypes allow for specific recognition of RNA motifs. Since targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses. PMID:23047683

Small-Molecule-Directed Hepatocyte-Like Cell Differentiation of Human Pluripotent Stem Cells.

PubMed

Mathapati, Santosh; Siller, Richard; Impellizzeri, Agata A R; Lycke, Max; Vegheim, Karianne; Almaas, Runar; Sullivan, Gareth J

2016-08-17

Hepatocyte-like cells (HLCs) generated in vitro from human pluripotent stem cells (hPSCs) provide an invaluable resource for basic research, regenerative medicine, drug screening, toxicology, and modeling of liver disease and development. This unit describes a small-molecule-driven protocol for in vitro differentiation of hPSCs into HLCs without the use of growth factors. hPSCs are coaxed through a developmentally relevant route via the primitive streak to definitive endoderm (DE) using the small molecule CHIR99021 (a Wnt agonist), replacing the conventional growth factors Wnt3A and activin A. The small-molecule-derived DE is then differentiated to hepatoblast-like cells in the presence of dimethyl sulfoxide. The resulting hepatoblasts are then differentiated to HLCs with N-hexanoic-Tyr, Ile-6 aminohexanoic amide (Dihexa, a hepatocyte growth factor agonist) and dexamethasone. The protocol provides an efficient and reproducible procedure for differentiation of hPSCs into HLCs utilizing small molecules. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo

NASA Astrophysics Data System (ADS)

Ye, Deju; Shuhendler, Adam J.; Cui, Lina; Tong, Ling; Tee, Sui Seng; Tikhomirov, Grigory; Felsher, Dean W.; Rao, Jianghong

2014-06-01

Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and already this has been used widely to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling the self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employ an optimized first-order bioorthogonal cyclization reaction to control the self-assembly of a fluorescent small molecule, and demonstrate its in vivo applicability by imaging caspase-3/7 activity in human tumour xenograft mouse models of chemotherapy. The fluorescent nanoparticles assembled in situ were imaged successfully in both apoptotic cells and tumour tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo.

9,10-Azaboraphenanthrene-containing small molecules and conjugated polymers: synthesis and their application in chemodosimeters for the ratiometric detection of fluoride ions.

PubMed

Zhang, Weidong; Li, Guoping; Xu, Letian; Zhuo, Yue; Wan, Wenming; Yan, Ni; He, Gang

2018-05-21

The introduction of main group elements into conjugated scaffolds is emerging as a key route to novel optoelectronic materials. Herein, an efficient and versatile way to synthesize polymerizable 9,10-azaboraphenanthrene ( BNP )-containing monomers by aromaticity-driven ring expansion reactions between highly antiaromatic borafluorene and azides is reported, and the corresponding conjugated small molecules and polymers are developed as well. The BNP -containing small molecules and conjugated polymers showed good air/moisture stability and notable fluorescence properties. Addition of fluoride ions to the BNP -based small molecules and polymers induced a rapid change in the emission color from blue to green/yellow, respectively, accompanied by strong intensity changes. The conjugated polymers showed better ratiometric sensing performance than small molecules due to the exciton migration along the conjugated chains. Further experiments showed that the sensing process is fully reversible. The films prepared by solution-deposition of BNP -based compounds in the presence of polycaprolactone also showed good ratiometric sensing for fluoride ions.

Small molecules enhance CRISPR genome editing in pluripotent stem cells.

PubMed

Yu, Chen; Liu, Yanxia; Ma, Tianhua; Liu, Kai; Xu, Shaohua; Zhang, Yu; Liu, Honglei; La Russa, Marie; Xie, Min; Ding, Sheng; Qi, Lei S

2015-02-05

The bacterial CRISPR-Cas9 system has emerged as an effective tool for sequence-specific gene knockout through non-homologous end joining (NHEJ), but it remains inefficient for precise editing of genome sequences. Here we develop a reporter-based screening approach for high-throughput identification of chemical compounds that can modulate precise genome editing through homology-directed repair (HDR). Using our screening method, we have identified small molecules that can enhance CRISPR-mediated HDR efficiency, 3-fold for large fragment insertions and 9-fold for point mutations. Interestingly, we have also observed that a small molecule that inhibits HDR can enhance frame shift insertion and deletion (indel) mutations mediated by NHEJ. The identified small molecules function robustly in diverse cell types with minimal toxicity. The use of small molecules provides a simple and effective strategy to enhance precise genome engineering applications and facilitates the study of DNA repair mechanisms in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity

DOE PAGES

Reznik, Ed; Christodoulou, Dimitris; Goldford, Joshua E.; ...

2017-09-12

Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurementsmore » and the SMRN to make inferences on the sensitivity of enzymes to their regulators. By generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.« less

Subsets of ATP-sensitive potassium channel (KATP) inhibitors increase gap junctional intercellular communication in metastatic cancer cell lines independent of SUR expression

USDA-ARS?s Scientific Manuscript database

Gap junctional intercellular communication (GJIC) is a process whereby cells share molecules and nutrients with each other by physical contact through cell membrane pores. In tumor cells, GJIC is often altered, suggesting that this process may be important in the context of cancer. Certain ion chan...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Yung-Ting; Department of Electrical Engineering, Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan 10617, Taiwan; Liu, Shun-Wei

Single-layer blue phosphorescence organic light emitting diodes (OLEDs) with either small-molecule or polymer hosts are fabricated using solution process and the performances of devices with different hosts are investigated. The small-molecule device exhibits luminous efficiency of 14.7 cd/A and maximum power efficiency of 8.39 lm/W, which is the highest among blue phosphorescence OLEDs with single-layer solution process and small molecular hosts. Using the same solution process for all devices, comparison of light out-coupling enhancement, with brightness enhancement film (BEF), between small-molecule and polymer based OLEDs is realized. Due to different dipole orientation and anisotropic refractive index, polymer-based OLEDs would trap less lightmore » than small molecule-based OLEDs internally, about 37% better based simulation results. In spite of better electrical and spectroscopic characteristics, including ambipolar characteristics, higher carrier mobility, higher photoluminescence quantum yield, and larger triplet state energy, the overall light out-coupling efficiency of small molecule-based devices is worse than that of polymer-based devices without BEF. However, with BEF for light out-coupling enhancement, the improved ratio in luminous flux and luminous efficiency for small molecule based device is 1.64 and 1.57, respectively, which are significantly better than those of PVK (poly-9-vinylcarbazole) devices. In addition to the theoretical optical simulation, the experimental data also confirm the origins of differential light-outcoupling enhancement. The maximum luminous efficiency and power efficiency are enhanced from 14.7 cd/A and 8.39 lm/W to 23 cd/A and 13.2 lm/W, respectively, with laminated BEF, which are both the highest so far for single-layer solution-process blue phosphorescence OLEDs with small molecule hosts.« less

The Arf GAP CNT-2 regulates the apoptotic fate in C. elegans asymmetric neuroblast divisions.

PubMed

Singhvi, Aakanksha; Teuliere, Jerome; Talavera, Karla; Cordes, Shaun; Ou, Guangshuo; Vale, Ronald D; Prasad, Brinda C; Clark, Scott G; Garriga, Gian

2011-06-07

During development, all cells make the decision to live or die. Although the molecular mechanisms that execute the apoptotic program are well defined, less is known about how cells decide whether to live or die. In C. elegans, this decision is linked to how cells divide asymmetrically [1, 2]. Several classes of molecules are known to regulate asymmetric cell divisions in metazoans, yet these molecules do not appear to control C. elegans divisions that produce apoptotic cells [3]. We identified CNT-2, an Arf GTPase-activating protein (GAP) of the AGAP family, as a novel regulator of this type of neuroblast division. Loss of CNT-2 alters daughter cell size and causes the apoptotic cell to adopt the fate of its sister cell, resulting in extra neurons. CNT-2's Arf GAP activity is essential for its function in these divisions. The N terminus of CNT-2, which contains a GTPase-like domain that defines the AGAP class of Arf GAPs, negatively regulates CNT-2's function. We provide evidence that CNT-2 regulates receptor-mediated endocytosis and consider the implications of its role in asymmetric cell divisions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Plasmonic Aptamer-Gold Nanoparticle Sensors for Small Molecule Fingerprint Identification

DTIC Science & Technology

2014-08-01

AFRL-RH-WP-TR-2014-0107 PLASMONIC APTAMER -GOLD NANOPARTICLE SENSORS FOR SMALL MOLECULE FINGERPRINT IDENTIFICATION Jorge Chávez Grant Slusher...Plasmonic Aptamer -Gold Nanoparticle Sensors for Small Molecule Fingerprint Identification 5a. CONTRACT NUMBER N/A 5b. GRANT NUMBER 5c. PROGRAM...The utilization of the plasmonic response of aptamer -gold nanoparticle conjugates (Apt-AuNPs) to design cross- reactive arrays for fingerprint

Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions.

PubMed

Guan, Lirui; Disney, Matthew D

2013-09-16

Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Re-education begins at home: an overview of the discovery of in vivo-active small molecule modulators of endogenous stem cells.

PubMed

Um, JungIn; Lee, Ji-Hyung; Jung, Da-Woon; Williams, Darren R

2018-04-01

Degenerative diseases, such as Alzheimer's disease, heart disease and arthritis cause great suffering and are major socioeconomic burdens. An attractive treatment approach is stem cell transplantation to regenerate damaged or destroyed tissues. However, this can be problematic. For example, donor cells may not functionally integrate into the host tissue. An alternative methodology is to deliver bioactive agents, such as small molecules, directly into the diseased tissue to enhance the regenerative potential of endogenous stem cells. Areas covered: In this review, the authors discuss the necessity of developing these small molecules to treat degenerative diseases and survey progress in their application as therapeutics. They describe both the successes and caveats of developing small molecules that target endogenous stem cells to induce tissue regeneration. This article is based on literature searches which encompass databases for biomedical research and clinical trials. These small molecules are also categorized per their target disease and mechanism of action. Expert opinion: The development of small molecules targeting endogenous stem cells is a high-profile research area. Some compounds have made the successful transition to the clinic. Novel approaches, such as modulating the stem cell niche or targeted delivery to disease sites, should increase the likelihood of future successes in this field.

Bottom-up design of small molecules that stimulate exon 10 skipping in mutant MAPT pre-mRNA.

PubMed

Luo, Yiling; Disney, Matthew D

2014-09-22

One challenge in chemical biology is to develop small molecules that control cellular protein content. The amount and identity of proteins are influenced by the RNAs that encode them; thus, protein content in a cell could be affected by targeting mRNA. However, RNA has been traditionally difficult to target with small molecules. In this report, we describe controlling the protein products of the mutated microtubule-associated protein tau (MAPT) mature mRNA with a small molecule. MAPT mutations in exon 10 are associated with inherited frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17), an incurable disease that is directly caused by increased inclusion of exon 10 in MAPT mRNA. Recent studies have shown that mutations within a hairpin at the MAPT exon 10-intron junction decrease the thermodynamic stability of the RNA, increasing binding to U1 snRNP and thus exon 10 inclusion. Therefore, we designed small molecules that bind and stabilize a mutant MAPT by using Inforna, a computational approach based on information about RNA-small-molecule interactions. The optimal compound selectively bound the mutant MAPT hairpin and thermodynamically stabilized its folding, facilitating exon 10 exclusion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small Molecule Supplements Improve Cultured Megakaryocyte Polyploidization by Modulating Multiple Cell Cycle Regulators.

PubMed

Zou, Xiaojing; Qu, Mingyi; Fang, Fang; Fan, Zeng; Chen, Lin; Yue, Wen; Xie, Xiaoyan; Pei, Xuetao

2017-01-01

Platelets (PLTs) are produced by megakaryocytes (MKs) that completed differentiation and endomitosis. Endomitosis is an important process in which the cell replicates its DNA without cytokinesis and develops highly polyploid MK. In this study, to gain a better PLTs production, four small molecules (Rho-Rock inhibitor (RRI), nicotinamide (NIC), Src inhibitor (SI), and Aurora B inhibitor (ABI)) and their combinations were surveyed as MK culture supplements for promoting polyploidization. Three leukemia cell lines as well as primary mononuclear cells were chosen in the function and mechanism studies of the small molecules. In an optimal culture method, cells were treated with different small molecules and their combinations. The impact of the small molecules on megakaryocytic surface marker expression, polyploidy, proliferation, and apoptosis was examined for the best MK polyploidization supplement. The elaborate analysis confirmed that the combination of SI and RRI together with our MK induction system might result in efficient ploidy promotion. Our experiments demonstrated that, besides direct downregulation on the expression of cytoskeleton protein actin, SI and RRI could significantly enhance the level of cyclins through the suppression of p53 and p21. The verified small molecule combination might be further used in the in vitro PLT manufacture and clinical applications.

Small Molecule Supplements Improve Cultured Megakaryocyte Polyploidization by Modulating Multiple Cell Cycle Regulators

PubMed Central

Fang, Fang; Chen, Lin; Yue, Wen

2017-01-01

Platelets (PLTs) are produced by megakaryocytes (MKs) that completed differentiation and endomitosis. Endomitosis is an important process in which the cell replicates its DNA without cytokinesis and develops highly polyploid MK. In this study, to gain a better PLTs production, four small molecules (Rho-Rock inhibitor (RRI), nicotinamide (NIC), Src inhibitor (SI), and Aurora B inhibitor (ABI)) and their combinations were surveyed as MK culture supplements for promoting polyploidization. Three leukemia cell lines as well as primary mononuclear cells were chosen in the function and mechanism studies of the small molecules. In an optimal culture method, cells were treated with different small molecules and their combinations. The impact of the small molecules on megakaryocytic surface marker expression, polyploidy, proliferation, and apoptosis was examined for the best MK polyploidization supplement. The elaborate analysis confirmed that the combination of SI and RRI together with our MK induction system might result in efficient ploidy promotion. Our experiments demonstrated that, besides direct downregulation on the expression of cytoskeleton protein actin, SI and RRI could significantly enhance the level of cyclins through the suppression of p53 and p21. The verified small molecule combination might be further used in the in vitro PLT manufacture and clinical applications. PMID:29201898

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors.

PubMed

Bucher, Tabitha; Kartvelishvily, Elena; Kolodkin-Gal, Ilana

2016-10-09

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.

Frontier molecular orbitals of a single molecule adsorbed on thin insulating films supported by a metal substrate: electron and hole attachment energies.

PubMed

Scivetti, Iván; Persson, Mats

2017-09-06

We present calculations of vertical electron and hole attachment energies to the frontier orbitals of a pentacene molecule absorbed on multi-layer sodium chloride films supported by a copper substrate using a simplified density functional theory (DFT) method. The adsorbate and the film are treated fully within DFT, whereas the metal is treated implicitly by a perfect conductor model. We find that the computed energy gap between the highest and lowest unoccupied molecular orbitals-HOMO and LUMO -from the vertical attachment energies increases with the thickness of the insulating film, in agreement with experiments. This increase of the gap can be rationalised in a simple dielectric model with parameters determined from DFT calculations and is found to be dominated by the image interaction with the metal. We find, however, that this simplified model overestimates the downward shift of the energy gap in the limit of an infinitely thick film.

Frontier molecular orbitals of a single molecule adsorbed on thin insulating films supported by a metal substrate: electron and hole attachment energies

NASA Astrophysics Data System (ADS)

Scivetti, Iván; Persson, Mats

2017-09-01

We present calculations of vertical electron and hole attachment energies to the frontier orbitals of a pentacene molecule absorbed on multi-layer sodium chloride films supported by a copper substrate using a simplified density functional theory (DFT) method. The adsorbate and the film are treated fully within DFT, whereas the metal is treated implicitly by a perfect conductor model. We find that the computed energy gap between the highest and lowest unoccupied molecular orbitals—HOMO and LUMO -from the vertical attachment energies increases with the thickness of the insulating film, in agreement with experiments. This increase of the gap can be rationalised in a simple dielectric model with parameters determined from DFT calculations and is found to be dominated by the image interaction with the metal. We find, however, that this simplified model overestimates the downward shift of the energy gap in the limit of an infinitely thick film.

Optoelectronic studies on heterocyclic bases of deoxyribonucleic acid for DNA photonics.

PubMed

El-Diasty, Fouad; Abdel-Wahab, Fathy

2015-10-01

The optoelectronics study of large molecules, particularly π-stacking molecules, such as DNA is really an extremely difficult task. We perform first electronic structure calculations on the heterocyclic bases of 2'-deoxyribonucleic acid based on Lorentz-Fresnel dispersion theory. In the UV-VIS range of spectrum, many of the optoelectronic parameters for DNA four bases namely adenine, guanine, cytosine and thymine are calculated and discussed. The results demonstrate that adenine has the highest hyperpolarizability, whereas thymine has the lowest hyperpolarizability. Cytosine has the lower average oscillator energy and the higher lattice energy. Thymine infers the most stable nucleic base with the lower phonon energy. Thymine also has the highest average oscillator energy and the lower lattice energy. Moreover, the four nucleic acid bases have large band gap energies less than 5 eV with a semiconducting behavior. Guanine shows the smallest band gap and the highest Fermi level energy, whereas adenine elucidates the highest band gap energy. Copyright © 2015. Published by Elsevier B.V.

Lovastatin inhibits gap junctional communication in cultured aortic smooth muscle cells.

PubMed

Shen, Jing; Wang, Li-Hong; Zheng, Liang-Rong; Zhu, Jian-Hua; Hu, Shen-Jiang

2010-09-01

Gap junctions, which serve as intercellular channels that allow the passage of ions and other small molecules between neighboring cells, play an important role in vital functions, including the regulation of cell growth, differentiation, and development. Statins, the 3-hydroxy-3-methylglutaryl-coenzymeA (HMG-CoA) reductase inhibitors, have been shown to inhibit the migration and proliferation of smooth muscle cells (SMCs) leading to an antiproliferative effect. Recent studies have shown that statins can reduce gap junction protein connexin43 (Cx43) expression both in vivo and in vitro. However, little work has been done on the effects of statins on gap junctional intercellular communication (GJIC). We hypothesized in this study that lovastatin inhibits vascular smooth muscle cells (VSMCs) migration through the inhibition of the GJIC. Rat aortic SMCs (RASMCs) were exposed to lovastatin. Vascular smooth muscle cells migration was then assessed with a Transwell migration assay. Gap junctional intercellular communication was determined by using fluorescence recovery after photobleaching (FRAP) analysis, which was performed with a laser-scanning confocal microscope. The migration of the cultured RASMCs were detected by Transwell system. Cell migration was dose-dependently inhibited with lovastatin. Compared with that in the control (110 ± 26), the number of migrated SMCs was significantly reduced to 72 ± 24 (P < .05), 62 ± 18 (P < .01), and 58 ± 19 (P < .01) at the concentration of 0.4, 2, and 10 umol/L, per field. The rate of fluorescence recovery (R) at 5 minutes after photobleaching was adopted as the functional index of GJIC. The R- value of cells exposed to lovastatin 10 umol/L for 48 hours was 24.38% ± 4.84%, whereas the cells in the control group had an R- value of 36.11% ± 10.53%, demonstrating that the GJIC of RASMCs was significantly inhibited by lovastatin (P < .01). Smaller concentrations of lovastatin 0.08 umol/L did not change gap junction coupling (P > .05). These results suggest that lovastatin inhibits migration in a dose-dependent manner by attenuating JIC. Suppression of gap junction function could add another explanation of statin-induced antiproliferative effect.

Exotic Molecules in Space: A Coordinated Astronomical Laboratory and Theoretical Study

NASA Technical Reports Server (NTRS)

Thaddeus, Patrick

1999-01-01

The past three years have been a period of great progress in our laboratory investigation of molecules of astrophysical interest-the most productive by far in the 20-year history of a research program which has led to the discovery of over 20% of the 123 known interstellar and circumstellar molecules. Most of the discoveries made during this period have been the result of the construction in late 1995 and early 1996 of a Fourier transform microwave spectrometer working in the centimeter-wave band. The sensitivity of this instrument from the moment that it was turned on has exceeded our expectations by an order of magnitude. The Table below shows the 46 new molecules which have been discovered. Most are carbon chains, the dominant type of molecule which has been found in space. Several comments with respect to these molecules should be made: 1. There are probably no mistakes in any of the identifications, since these have been confirmed by the standard, powerful assays and tests used to check spectroscopic identifications: isotopic substitution, quantum calculations of the expected molecular structures, detection of hyperfine structure, Zeeman effect, etc. 2. The radio laboratory astrophysics of the entire set is complete for the time being, in the sense that essentially all the astronomically interesting radio transitions (including hfs when present) are either directly measured or can now be calculated from the derived spectroscopic constants to better than 1 part per million (or 0.3 km s-1 in radial velocity, and often much better than that). 3. Six of the forty six new molecules have already been identified in space, in every case but one on the basis of our laboratory measurements. 4. Sensitive as they are, our laboratory techniques are far from fundamental limits on sensitivity, and 5. One of the principal motivations of our research is to close the fairly small mass and size gap, now only a factor of a few, between the smallest postulated interstellar grains and the largest identified interstellar molecules.

Trade-off between competition and facilitation defines gap colonization in mountains

PubMed Central

Lembrechts, Jonas J.; Milbau, Ann; Nijs, Ivan

2015-01-01

Recent experimental observations show that gap colonization in small-stature (e.g. grassland and dwarf shrubs) vegetation strongly depends on the abiotic conditions within them. At the same time, within-gap variation in biotic interactions such as competition and facilitation, caused by distance to the gap edge, would affect colonizer performance, but a theoretical framework to explore such patterns is missing. Here, we model how competition, facilitation and environmental conditions together determine the small-scale patterns of gap colonization along a cold gradient in mountains, by simulating colonizer survival in gaps of various sizes. Our model adds another dimension to the known effects of biotic interactions along a stress gradient by focussing on the trade-off between competition and facilitation in the within-gap environment. We show that this trade-off defines a peak in colonizer survival at a specific distance from the gap edge, which progressively shifts closer to the edge as the environment gets colder, ultimately leaving a large fraction of gaps unsuitable for colonization in facilitation-dominated systems. This is reinforced when vegetation size and temperature amelioration are manipulated simultaneously with temperature in order to simulate an elevational gradient more realistically. Interestingly, all other conditions being equal, the magnitude of the realized survival peak was always lower in large than in small gaps, making large gaps harder to colonize. The model is relevant to predict effects of non-native plant invasions and climate warming on colonization processes in mountains. PMID:26558706

The Role of the Superintendent in Closing the Achievement Gap in Diverse Small School Districts

ERIC Educational Resources Information Center

Wright, Howell, Jr.; Harris, Sandra

2010-01-01

The purpose of this qualitative, narrative study was to investigate the role of the superintendent in leading the district to be more culturally proficient, resulting in the narrowing of the achievement gap in culturally diverse small districts. Eight superintendents of small school districts were purposefully selected based on their district size…

Study of the electronic structure of electron accepting cyano-films: TCNQversusTCNE.

PubMed

Capitán, Maria J; Álvarez, Jesús; Navio, Cristina

2018-04-18

In this article, we perform systematic research on the electronic structure of two closely related organic electron acceptor molecules (TCNQ and TCNE), which are of technological interest due to their outstanding electronic properties. These studies have been performed from the experimental point of view by the use electron spectroscopies (XPS and UPS) and supported theoretically by the use of ab-initio DFT calculations. The cross-check between both molecules allows us to identify the characteristic electronic features of each part of the molecules and their contribution to the final electronic structure. We can describe the nature of the band gap of these materials, and we relate this with the appearance of the shake-up features in the core level spectra. A band bending and energy gap reduction of the aforementioned electronic structure in contact with a metal surface are seen in the experimental results as well in the theoretical calculations. This behavior implies that the TCNQ thin film accepts electrons from the metal substrate becoming a Schottky n-junction.

Optical response tuning in nanorod-on-semicontinous film systems: A computational study

NASA Astrophysics Data System (ADS)

Mokkath, Junais Habeeb

2018-01-01

Strongly confined and intense optical fields within the plasmonic metal nanocavities show outstanding potential for a wide range of functionalities in nanophotonics. Using time dependent density functional theory calculations, we investigate the optical response evolution as a function of the gap separation distances in nanorod-on-film systems comprised of a nanorod (NR) made of Al or Na on top of an Al film. Huge optical field modulations emerged in the chemically distinct Na NR - Al film system in comparison to the Al NR - Al film system, indicating the vital role of metals involved. We further study the optical response modifications by placing a conducting molecule in the gap region, finding strong spectral modulations via through-molecule electron tunneling.

Electronic Structure of Small Lanthanide Containing Molecules

NASA Astrophysics Data System (ADS)

Kafader, Jared O.; Ray, Manisha; Topolski, Josey E.; Chick Jarrold, Caroline

2016-06-01

Lanthanide-based materials have unusual electronic properties because of the high number of electronic degrees of freedom arising from partial occupation of 4f orbitals, which make these materials optimal for their utilization in many applications including electronics and catalysis. Electronic spectroscopy of small lanthanide molecules helps us understand the role of these 4f electrons, which are generally considered core-like because of orbital contraction, but are energetically similar to valence electrons. The spectroscopy of small lanthanide-containing molecules is relatively unexplored and to broaden this understanding we have completed the characterization of small cerium, praseodymium, and europium molecules using photoelectron spectroscopy coupled with DFT calculations. The characterization of PrO, EuH, EuO/EuOH, and CexOy molecules have allowed for the determination of their electron affinity, the assignment of numerous anion to neutral state transitions, modeling of anion/neutral structures and electron orbital occupation.

System dynamics of subcellular transport.

PubMed

Chen, Vivien Y; Khersonsky, Sonya M; Shedden, Kerby; Chang, Young Tae; Rosania, Gus R

2004-01-01

In pharmacokinetic experiments, interpretations often hinge on treating cells as a "black box": a single, lumped compartment or boundary. Here, a combinatorial library of fluorescent small molecules was used to visualize subcellular transport pathways in living cells, using a kinetic, high content imaging system to monitor spatiotemporal variations of intracellular probe distribution. Most probes accumulate in cytoplasmic vesicles and probe kinetics conform to a nested, two-compartment dynamical system. At steady state, probes preferentially partition from the extracellular medium to the cytosol, and from the cytosol to cytoplasmic vesicles, with hydrophobic molecules favoring sequestration. Altogether, these results point to a general organizing principle underlying the system dynamics of subcellular, small molecule transport. In addition to plasma membrane permeability, subcellular transport phenomena can determine the active concentration of small molecules in the cytosol and the efflux of small molecules from cells. Fundamentally, direct observation of intracellular probe distribution challenges the simple boundary model of classical pharmacokinetics, which considers cells as static permeability barriers.

Hot-Volumes as Uniform and Reproducible SERS-Detection Enhancers in Weakly-Coupled Metallic Nanohelices

NASA Astrophysics Data System (ADS)

Caridad, José M.; Winters, Sinéad; McCloskey, David; Duesberg, Georg S.; Donegan, John F.; Krstić, Vojislav

2017-03-01

Reproducible and enhanced optical detection of molecules in low concentrations demands simultaneously intense and homogeneous electric fields acting as robust signal amplifiers. To generate such sophisticated optical near-fields, different plasmonic nanostructures were investigated in recent years. These, however, exhibit either high enhancement factor (EF) or spatial homogeneity but not both. Small interparticle gaps or sharp nanostructures show enormous EFs but no near-field homogeneity. Meanwhile, approaches using rounded and separated monomers create uniform near-fields with moderate EFs. Here, guided by numerical simulations, we show how arrays of weakly-coupled Ag nanohelices achieve both homogeneous and strong near-field enhancements, reaching even the limit forreproducible detection of individual molecules. The unique near-field distribution of a single nanohelix consists of broad hot-spots, merging with those from neighbouring nanohelices in specific array configurations and generating a wide and uniform detection zone (“hot-volume”). We experimentally assessed these nanostructures via surface-enhanced Raman spectroscopy, obtaining a corresponding EF of ~107 and a relative standard deviation <10%. These values demonstrate arrays of nanohelices as state-of-the-art substrates for reproducible optical detection as well as compelling nanostructures for related fields such as near-field imaging.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Activation of Polymine Catabolism as a Novel Strategy for Treating and/or Preventing Human Prostate Cancer

DTIC Science & Technology

2006-03-01

strategy against prostate cancer and thus, worthy of small molecule discovery and development. On the basis of findings obtained over the past 3...support for the discovery and development of specific small molecule inducers of SSAT as a novel therapeutic strategy targeting prostate cancer. This...D. Unscheduled Findings. Findings under Tasks 1 and 3 provided genetic evidence for the discovery and development of small molecule inducers of

A-D-A small molecules for solution-processed organic photovoltaic cells.

PubMed

Ni, Wang; Wan, Xiangjian; Li, Miaomiao; Wang, Yunchuang; Chen, Yongsheng

2015-03-25

A-D-A small molecules have drawn more and more attention in solution-processed organic solar cells due to the advantages of a diversity of structures, easy control of energy levels, etc. Recently, a power conversion efficiency of nearly 10% has been achieved through careful material design and device optimization. This feature article reviews recent representative progress in the design and application of A-D-A small molecules in organic photovoltaic cells.

Delivery of small molecules for bone regenerative engineering: preclinical studies and potential clinical applications

PubMed Central

Laurencin, Cato T.; Ashe, Keshia M.; Henry, Nicole; Kan, Ho Man; Lo, Kevin W-H.

2014-01-01

Stimulation of bone regeneration using growth factors is a promising approach for musculoskeletal regenerative engineering. Common limitations with protein growth factors are high manufacturing costs, protein instability, contamination issues, and unwanted immunogenic responses of the host. New strategies for bone regeneration that obviate these problems can have a significant impact on the treatment of skeletal injury and diseases. Over the past decade, a large number of small molecules with the potential of regenerating skeletal tissue have been reported in the literature. Here, we review this literature, paying specific attention to the prospects for small molecule-based bone-regenerative engineering. We also review the preclinical study of small molecules associated with bone regeneration. PMID:24508820

Cobalt coated substrate for matrix-free analysis of small molecules by laser desorption/ionization mass spectrometry

NASA Astrophysics Data System (ADS)

Yalcin, Talat; Li, Liang

2009-12-01

Small molecule analysis is one of the most challenging issues in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. We have developed a cobalt coated substrate as a target for matrix-free analysis of small molecules in laser desorption/ionization mass spectrometry. Cobalt coating of 60-70 nm thickness has been characterized by scanning electron microscopy, energy dispersive X-ray analysis, X-ray diffraction, and laser induced breakdown spectroscopy. This target facilitates hundreds of samples to be spotted and analyzed without mixing any matrices, in a very short time. This can save a lot of time and money and can be a very practical approach for the analysis of small molecules by laser desorption/ionization mass spectrometry.

Combinatorics of feedback in cellular uptake and metabolism of small molecules.

PubMed

Krishna, Sandeep; Semsey, Szabolcs; Sneppen, Kim

2007-12-26

We analyze the connection between structure and function for regulatory motifs associated with cellular uptake and usage of small molecules. Based on the boolean logic of the feedback we suggest four classes: the socialist, consumer, fashion, and collector motifs. We find that the socialist motif is good for homeostasis of a useful but potentially poisonous molecule, whereas the consumer motif is optimal for nutrition molecules. Accordingly, examples of these motifs are found in, respectively, the iron homeostasis system in various organisms and in the uptake of sugar molecules in bacteria. The remaining two motifs have no obvious analogs in small molecule regulation, but we illustrate their behavior using analogies to fashion and obesity. These extreme motifs could inspire construction of synthetic systems that exhibit bistable, history-dependent states, and homeostasis of flux (rather than concentration).

The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy

PubMed Central

Kötting, Carsten; Kallenbach, Angela; Suveyzdis, Yan; Wittinghofer, Alfred; Gerwert, Klaus

2008-01-01

Members of the Ras superfamily of small G proteins play key roles in signal transduction pathways, which they control by GTP hydrolysis. They are regulated by GTPase activating proteins (GAPs). Mutations that prevent hydrolysis cause severe diseases including cancer. A highly conserved “arginine finger” of GAP is a key residue. Here, we monitor the GTPase reaction of the Ras·RasGAP complex at high temporal and spatial resolution by time-resolved FTIR spectroscopy at 260 K. After triggering the reaction, we observe as the first step a movement of the switch-I region of Ras from the nonsignaling “off” to the signaling “on” state with a rate of 3 s−1. The next step is the movement of the “arginine finger” into the active site of Ras with a rate of k2 = 0.8 s−1. Once the arginine points into the binding pocket, cleavage of GTP is fast and the protein-bound Pi intermediate forms. The switch-I reversal to the “off” state, the release of Pi, and the movement of arginine back into an aqueous environment is observed simultaneously with k3 = 0.1 s−1, the rate-limiting step. Arrhenius plots for the partial reactions show that the activation energy for the cleavage reaction is lowered by favorable positive activation entropy. This seems to indicate that protein-bound structured water molecules are pushed by the “arginine finger” movement out of the binding pocket into the bulk water. The proposed mechanism shows how the high activation barrier for phosphoryl transfer can be reduced by splitting into partial reactions separated by a Pi-intermediate. PMID:18434546

Density functional theory design D-D-A type small molecule with 1.03 eV narrow band gap: effect of electron donor unit for organic photovoltaic solar cell

NASA Astrophysics Data System (ADS)

Sıdır, İsa

2017-10-01

Six new low-band-gap copolymers of donor-donor-acceptor (D-D-A) architecture have been designed using density functional theory and time-dependent density functional theory methods in order to use them in organic photovoltaic cell (OPVC). Phenanthro[3,4-d:9,10-d‧]bis([1,2,3]thiadiazole)-10,12-dicarbonitrile moiety has been used as an acceptor for all compounds. We insert benzo[1,2-b:4,5-b‧]dithiophene and N,N-diphenylbenzo[1,2-b:4,5-b‧]dithiophen-2-amine units as donor to complete designing of copolymers. In order to tuning the optical and electronic properties, we have modified the donor unit by substituted with amine, methoxyamine, N-methylenethiophen-2-amine, methoxy, alkoxy moieties. The band gap (Eg), HOMO and LUMO values and plots, open circuit voltage (VOC) as well as optical properties have been analysed for designed copolymers. The optimised copolymers exhibit low-band-gap lying in the range of 1.03-2.24 eV. DPTD-6 copolymer presents the optimal properties to be used as an active layer due to its low Eg (1.03 eV) and a moderate VOC (0.56 eV). Thus, OPVC based on this copolymer in bulk-heterojunction composites with [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) as an acceptor has been modelled. Eg and VOC values of composite material DPTD-6:PCBM are found as 1.32 and 0.65 eV, respectively. A model band diagram has been established for OPVC, simulating the energy transfer between active layers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xuan; Deeb, Claire; Kostcheev, Sergei

We report a self-developing anisotropic gold/polymer hybrid nanosystem that precisely places dye molecules at the plasmonic hotspot of metal nanostructures for sensing and photonics applications. Unlike conventional molecule-particle configurations, the anisotropic hybrid nanosystem (AHN) introduces an anisotropic spatial distribution of dye-containing active medium. This allows us to precisely overlap the near-field spatial distribution with the active medium and rule out the contribution from the background molecules. This overlap effect selectively highlights the optical response of the molecules of interest, i.e., molecules located at the hotspots. Our AHN consists of gold nanodimers whose gaps have been filled with methylene blue molecules.more » They have been studied by plasmon-enhanced Raman spectroscopy as a probing tool. The AHN opens new doors not only for fundamental studies and photonics applications of molecule-particle interactions, but also for molecular trapping methods at the nanoscale.« less

Free energy barriers to evaporation of water in hydrophobic confinement.

PubMed

Sharma, Sumit; Debenedetti, Pablo G

2012-11-08

We use umbrella sampling Monte Carlo and forward and reverse forward flux sampling (FFS) simulation techniques to compute the free energy barriers to evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of the gap width, at 1 bar and 298 K. The evaporation mechanism for small (1 × 1 nm(2)) surfaces is found to be fundamentally different from that for large (3 × 3 nm(2)) surfaces. In the latter case, the evaporation proceeds via the formation of a gap-spanning tubular cavity. The 1 × 1 nm(2) surfaces, in contrast, are too small to accommodate a stable vapor cavity. Accordingly, the associated free energy barriers correspond to the formation of a critical-sized cavity for sufficiently large confining surfaces, and to complete emptying of the gap region for small confining surfaces. The free energy barriers to evaporation were found to be of O(20kT) for 14 Å gaps, and to increase by approximately ~5kT with every 1 Å increase in the gap width. The entropy contribution to the free energy of evaporation was found to be independent of the gap width.

Effects of the charge-transfer reorganization energy on the open-circuit voltage in small-molecular bilayer organic photovoltaic devices: comparison of the influence of deposition rates of the donor.

PubMed

Lee, Chih-Chien; Su, Wei-Cheng; Chang, Wen-Chang

2016-05-14

The theoretical maximum of open-circuit voltage (VOC) of organic photovoltaic (OPV) devices has yet to be determined, and its origin remains debated. Here, we demonstrate that VOC of small-molecule OPV devices can be improved by controlling the deposition rate of a donor without changing the interfacial energy gap at the donor/acceptor interface. The measurement of external quantum efficiency and electroluminescence spectra facilitates the observation of the existence of charge transfer (CT) states. A simplified approach by reusing the reciprocity relationship for obtaining the properties of the CT states is proposed without introducing complex techniques. We compare experimental and fitting results and propose that reorganization energy is the primary factor in determining VOC instead of either the CT energy or electronic coupling term in bilayer OPV devices. Atomic force microscopy images indicate a weak molecular aggregation when a higher deposition rate is used. The results of temperature-dependent measurements suggest the importance of molecular stacking for the CT properties.

Thymic selection threshold defined by compartmentalization of Ras/MAPK signalling.

PubMed

Daniels, Mark A; Teixeiro, Emma; Gill, Jason; Hausmann, Barbara; Roubaty, Dominique; Holmberg, Kaisa; Werlen, Guy; Holländer, Georg A; Gascoigne, Nicholas R J; Palmer, Ed

2006-12-07

A healthy individual can mount an immune response to exogenous pathogens while avoiding an autoimmune attack on normal tissues. The ability to distinguish between self and non-self is called 'immunological tolerance' and, for T lymphocytes, involves the generation of a diverse pool of functional T cells through positive selection and the removal of overtly self-reactive thymocytes by negative selection during T-cell ontogeny. To elucidate how thymocytes arrive at these cell fate decisions, here we have identified ligands that define an extremely narrow gap spanning the threshold that distinguishes positive from negative selection. We show that, at the selection threshold, a small increase in ligand affinity for the T-cell antigen receptor leads to a marked change in the activation and subcellular localization of Ras and mitogen-activated protein kinase (MAPK) signalling intermediates and the induction of negative selection. The ability to compartmentalize signalling molecules differentially in the cell endows the thymocyte with the ability to convert a small change in analogue input (affinity) into a digital output (positive versus negative selection) and provides the basis for establishing central tolerance.

Development of biosensors and their application in metabolic engineering.

PubMed

Zhang, Jie; Jensen, Michael K; Keasling, Jay D

2015-10-01

In a sustainable bioeconomy, many commodities and high value chemicals, including pharmaceuticals, will be manufactured using microbial cell factories from renewable feedstocks. These cell factories can be efficiently generated by constructing libraries of diversified genomes followed by screening for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule binding and ease of implementation with high-throughput analysis. Here we describe recent progress in biosensor development and their applications in a metabolic engineering context. We also highlight examples of how biosensors can be integrated with synthetic circuits to exert feedback regulation on the metabolism for improved performance of cell factories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts.

PubMed

Kumar, Amit; Parkesh, Raman; Sznajder, Lukasz J; Childs-Disney, Jessica L; Sobczak, Krzysztof; Disney, Matthew D

2012-03-16

Recently, it was reported that expanded r(CAG) triplet repeats (r(CAG)(exp)) associated with untreatable neurological diseases cause pre-mRNA mis-splicing likely due to sequestration of muscleblind-like 1 (MBNL1) splicing factor. Bioactive small molecules that bind the 5'CAG/3'GAC motif found in r(CAG)(exp) hairpin structure were identified by using RNA binding studies and virtual screening/chemical similarity searching. Specifically, a benzylguanidine-containing small molecule was found to improve pre-mRNA alternative splicing of MBNL1-sensitive exons in cells expressing the toxic r(CAG)(exp). The compound was identified by first studying the binding of RNA 1 × 1 nucleotide internal loops to small molecules known to have affinity for nucleic acids. Those studies identified 4',6-diamidino-2-phenylindole (DAPI) as a specific binder to RNAs with the 5'CAG/3'GAC motif. DAPI was then used as a query molecule in a shape- and chemistry alignment-based virtual screen to identify compounds with improved properties, which identified 4-guanidinophenyl 4-guanidinobenzoate, a small molecule that improves pre-mRNA splicing defects associated with the r(CAG)(exp)-MBNL1 complex. This compound may facilitate the development of therapeutics to treat diseases caused by r(CAG)(exp) and could serve as a useful chemical tool to dissect the mechanisms of r(CAG)(exp) toxicity. The approach used in these studies, defining the small RNA motifs that bind small molecules with known affinity for nucleic acids and then using virtual screening to optimize them for bioactivity, may be generally applicable for designing small molecules that target other RNAs in the human genomic sequence.

A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces.

PubMed

Xu, David; Si, Yubing; Meroueh, Samy O

2017-09-25

The binding affinity of a protein-protein interaction is concentrated at amino acids known as hot spots. It has been suggested that small molecules disrupt protein-protein interactions by either (i) engaging receptor protein hot spots or (ii) mimicking hot spots of the protein ligand. Yet, no systematic studies have been done to explore how effectively existing small-molecule protein-protein interaction inhibitors mimic or engage hot spots at protein interfaces. Here, we employ explicit-solvent molecular dynamics simulations and end-point MM-GBSA free energy calculations to explore this question. We select 36 compounds for which high-quality binding affinity and cocrystal structures are available. Five complexes that belong to three classes of protein-protein interactions (primary, secondary, and tertiary) were considered, namely, BRD4•H4, XIAP•Smac, MDM2•p53, Bcl-xL•Bak, and IL-2•IL-2Rα. Computational alanine scanning using MM-GBSA identified hot-spot residues at the interface of these protein interactions. Decomposition energies compared the interaction of small molecules with individual receptor hot spots to those of the native protein ligand. Pharmacophore analysis was used to investigate how effectively small molecules mimic the position of hot spots of the protein ligand. Finally, we study whether small molecules mimic the effects of the native protein ligand on the receptor dynamics. Our results show that, in general, existing small-molecule inhibitors of protein-protein interactions do not optimally mimic protein-ligand hot spots, nor do they effectively engage protein receptor hot spots. The more effective use of hot spots in future drug design efforts may result in smaller compounds with higher ligand efficiencies that may lead to greater success in clinical trials.

Cancer Theranostic Nanoparticles Self-Assembled from Amphiphilic Small Molecules with Equilibrium Shift-Induced Renal Clearance

PubMed Central

Ma, Yuan; Mou, Quanbing; Sun, Mo; Yu, Chunyang; Li, Jianqi; Huang, Xiaohua; Zhu, Xinyuan; Yan, Deyue; Shen, Jian

2016-01-01

Nano drug delivery systems have emerged as promising candidates for cancer therapy, whereas their uncertainly complete elimination from the body within specific timescales restricts their clinical translation. Compared with hepatic clearance of nanoparticles, renal excretion of small molecules is preferred to minimize the agent-induced toxicity. Herein, we construct in vivo renal-clearable nanoparticles, which are self-assembled from amphiphilic small molecules holding the capabilities of magnetic resonance imaging (MRI) and chemotherapy. The assembled nanoparticles can accumulate in tumor tissues for their nano-characteristics, while the small molecules dismantled from the nanoparticles can be efficiently cleared by kidneys. The renal-clearable nanoparticles exhibit excellent tumor-inhibition performance as well as low side effects and negligible chronic toxicity. These results demonstrate a potential strategy for small molecular nano drug delivery systems with obvious anticancer effect and low-toxic metabolism pathway for clinical applications. PMID:27446502

Ambipolar nature of dimethyl benzo difuran (DMBDF) molecule: A charge transport study

NASA Astrophysics Data System (ADS)

Sahoo, Smruti Ranjan; Sahu, Sridhar

2017-05-01

We describe a theoretical study of the charge transport properties of the organic dimethyl benzo difuran (DMBDF) molecule based on density functional theory (DFT). Reorganization energy, ionization potential (IP), electron affinity (EA), energy gaps, transfer integral (t) and charge mobility (μ) has been studied to depict the transport properties in the conjugated organic molecules. We computed, large homo transfer integral and IP value leading to high hole mobility (4.46 cm2/V sec). However, the electron reorganization energy (0.34 eV) and the electron mobility of 1.62 cm2/V sec, infers that the DMBDF organic molecule bears an ambipolar character.

Single-Molecule Bioelectronics

PubMed Central

Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

2014-01-01

Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

Trade-off between competition and facilitation defines gap colonization in mountains.

PubMed

Lembrechts, Jonas J; Milbau, Ann; Nijs, Ivan

2015-11-10

Recent experimental observations show that gap colonization in small-stature (e.g. grassland and dwarf shrubs) vegetation strongly depends on the abiotic conditions within them. At the same time, within-gap variation in biotic interactions such as competition and facilitation, caused by distance to the gap edge, would affect colonizer performance, but a theoretical framework to explore such patterns is missing. Here, we model how competition, facilitation and environmental conditions together determine the small-scale patterns of gap colonization along a cold gradient in mountains, by simulating colonizer survival in gaps of various sizes. Our model adds another dimension to the known effects of biotic interactions along a stress gradient by focussing on the trade-off between competition and facilitation in the within-gap environment. We show that this trade-off defines a peak in colonizer survival at a specific distance from the gap edge, which progressively shifts closer to the edge as the environment gets colder, ultimately leaving a large fraction of gaps unsuitable for colonization in facilitation-dominated systems. This is reinforced when vegetation size and temperature amelioration are manipulated simultaneously with temperature in order to simulate an elevational gradient more realistically. Interestingly, all other conditions being equal, the magnitude of the realized survival peak was always lower in large than in small gaps, making large gaps harder to colonize. The model is relevant to predict effects of non-native plant invasions and climate warming on colonization processes in mountains. Published by Oxford University Press on behalf of the Annals of Botany Company.

Effects of endogenous small molecular compounds on the rheological properties, texture and microstructure of soymilk coagulum: Removal of phytate using ultrafiltration.

PubMed

Wang, Ruican; Guo, Shuntang

2016-11-15

This study aims to clarify the roles played by endogenous small molecular components in soymilk coagulation process and the properties of gels. Soymilk samples with decreasing levels of small molecules were prepared by ultrafiltration, to reduce the amount of phytate and salts. CaSO4-induced coagulation process was analyzed using rheological methods. Results showed that removal of free small molecules decreased the activation energy of protein coagulation, resulting in accelerated reaction and increased gel strength. However, too fast a reaction led to the drop in storage modulus (G'). Microscopic observation suggested that accelerated coagulation generated a coarse and non-uniform gel network with large pores. This network could not hold much water, leading to serious syneresis. Endogenous small molecules in soymilk were vital in the fine gel structure. Coagulation rate could be controlled by adjusting the amount of small molecules to obtain tofu products with the optimal texture. Copyright © 2016 Elsevier Ltd. All rights reserved.

Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules.

PubMed

Childs-Disney, Jessica L; Stepniak-Konieczna, Ewa; Tran, Tuan; Yildirim, Ilyas; Park, HaJeung; Chen, Catherine Z; Hoskins, Jason; Southall, Noel; Marugan, Juan J; Patnaik, Samarjit; Zheng, Wei; Austin, Chris P; Schatz, George C; Sobczak, Krzysztof; Thornton, Charles A; Disney, Matthew D

2013-01-01

The ability to control pre-mRNA splicing with small molecules could facilitate the development of therapeutics or cell-based circuits that control gene function. Myotonic dystrophy type 1 is caused by the dysregulation of alternative pre-mRNA splicing due to sequestration of muscleblind-like 1 protein (MBNL1) by expanded, non-coding r(CUG) repeats (r(CUG)(exp)). Here we report two small molecules that induce or ameliorate alternative splicing dysregulation. A thiophene-containing small molecule (1) inhibits the interaction of MBNL1 with its natural pre-mRNA substrates. Compound (2), a substituted naphthyridine, binds r(CUG)(exp) and displaces MBNL1. Structural models show that 1 binds MBNL1 in the Zn-finger domain and that 2 interacts with UU loops in r(CUG)(exp). This study provides a structural framework for small molecules that target MBNL1 by mimicking r(CUG)(exp) and shows that targeting MBNL1 causes dysregulation of alternative splicing, suggesting that MBNL1 is thus not a suitable therapeutic target for the treatment of myotonic dystrophy type 1.

Induction and Reversal of Myotonic Dystrophy Type 1 Pre-mRNA Splicing Defects by Small Molecules

PubMed Central

Childs-Disney, Jessica L.; Stepniak-Konieczna, Ewa; Tran, Tuan; Yildirim, Ilyas; Park, HaJeung; Chen, Catherine Z.; Hoskins, Jason; Southall, Noel; Marugan, Juan J.; Patnaik, Samarjit; Zheng, Wei; Austin, Chris P.; Schatz, George C.; Sobczak, Krzysztof; Thornton, Charles A.; Disney, Matthew D.

2013-01-01

The ability to control pre-mRNA splicing with small molecules could facilitate the development of therapeutics or cell-based circuits that control gene function. Myotonic dystrophy type 1 (DM1) is caused by the dysregulation of alternative pre-mRNA splicing due to sequestration of muscleblind-like 1 protein (MBNL1) by expanded, non-coding r(CUG) repeats (r(CUG)exp). Here we report two small molecules that induce or ameliorate alternative splicing dysregulation. The thiophene-containing small molecule (1) inhibits the interaction of MBNL1 with its natural pre-mRNA substrates. Compound (2), a substituted naphthyridine, binds r(CUG)exp and displaces MBNL1. Structural models show that 1 binds MBNL1 in the Zn-finger domain and that 2 interacts with UU loops in r(CUG)exp. This study provides a structural framework for small molecules that target MBNL1 by mimicking r(CUG)exp and shows that targeting MBNL1 causes dysregulation of alternative splicing, suggesting that MBNL1 is thus not a suitable therapeutic target for the treatment of DM1. PMID:23806903

Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening

PubMed Central

Dandapani, Sivaraman; Rosse, Gerard; Southall, Noel; Salvino, Joseph M.; Thomas, Craig J.

2015-01-01

The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition. PMID:26705509

Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening.

PubMed

Dandapani, Sivaraman; Rosse, Gerard; Southall, Noel; Salvino, Joseph M; Thomas, Craig J

The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.

Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines.

PubMed

Zhang, Xinyuan; Zheng, Nan; Rosania, Gus R

2008-09-01

Cell-based molecular transport simulations are being developed to facilitate exploratory cheminformatic analysis of virtual libraries of small drug-like molecules. For this purpose, mathematical models of single cells are built from equations capturing the transport of small molecules across membranes. In turn, physicochemical properties of small molecules can be used as input to simulate intracellular drug distribution, through time. Here, with mathematical equations and biological parameters adjusted so as to mimic a leukocyte in the blood, simulations were performed to analyze steady state, relative accumulation of small molecules in lysosomes, mitochondria, and cytosol of this target cell, in the presence of a homogenous extracellular drug concentration. Similarly, with equations and parameters set to mimic an intestinal epithelial cell, simulations were also performed to analyze steady state, relative distribution and transcellular permeability in this non-target cell, in the presence of an apical-to-basolateral concentration gradient. With a test set of ninety-nine monobasic amines gathered from the scientific literature, simulation results helped analyze relationships between the chemical diversity of these molecules and their intracellular distributions.

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

PubMed

Fang, Mingliang; Ivanisevic, Julijana; Benton, H Paul; Johnson, Caroline H; Patti, Gary J; Hoang, Linh T; Uritboonthai, Winnie; Kurczy, Michael E; Siuzdak, Gary

2015-11-03

Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online ( xcmsonline.scripps.edu ). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo significant time-sensitive alterations when exposed to elevated temperatures, especially those conditions that mimic sample preparation and analysis in GC/MS experiments.

Identification of small molecules capable of regulating conformational changes of telomeric G-quadruplex

NASA Astrophysics Data System (ADS)

Chen, Shuo-Bin; Liu, Guo-Cai; Gu, Lian-Quan; Huang, Zhi-Shu; Tan, Jia-Heng

2018-02-01

Design of small molecules targeted at human telomeric G-quadruplex DNA is an extremely active research area. Interestingly, the telomeric G-quadruplex is a highly polymorphic structure. Changes in its conformation upon small molecule binding may be a powerful method to achieve a desired biological effect. However, the rational development of small molecules capable of regulating conformational change of telomeric G-quadruplex structures is still challenging. In this study, we developed a reliable ligand-based pharmacophore model based on isaindigotone derivatives with conformational change activity toward telomeric G-quadruplex DNA. Furthermore, virtual screening of database was conducted using this pharmacophore model and benzopyranopyrimidine derivatives in the database were identified as a strong inducer of the telomeric G-quadruplex DNA conformation, transforming it from hybrid-type structure to parallel structure.

Protein Scaffolding for Small Molecule Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, David

We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematicallymore » modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.« less

SPLINTS: small-molecule protein ligand interface stabilizers.

PubMed

Fischer, Eric S; Park, Eunyoung; Eck, Michael J; Thomä, Nicolas H

2016-04-01

Regulatory protein-protein interactions are ubiquitous in biology, and small molecule protein-protein interaction inhibitors are an important focus in drug discovery. Remarkably little attention has been given to the opposite strategy-stabilization of protein-protein interactions, despite the fact that several well-known therapeutics act through this mechanism. From a structural perspective, we consider representative examples of small molecules that induce or stabilize the association of protein domains to inhibit, or alter, signaling for nuclear hormone, GTPase, kinase, phosphatase, and ubiquitin ligase pathways. These SPLINTS (small-molecule protein ligand interface stabilizers) drive interactions that are in some cases physiologically relevant, and in others entirely adventitious. The diverse structural mechanisms employed suggest approaches for a broader and systematic search for such compounds in drug discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Selective small-molecule inhibitors as chemical tools to define the roles of matrix metalloproteinases in disease.

PubMed

Meisel, Jayda E; Chang, Mayland

2017-11-01

The focus of this article is to highlight novel inhibitors and current examples where the use of selective small-molecule inhibitors has been critical in defining the roles of matrix metalloproteinases (MMPs) in disease. Selective small-molecule inhibitors are surgical chemical tools that can inhibit the targeted enzyme; they are the method of choice to ascertain the roles of MMPs and complement studies with knockout animals. This strategy can identify targets for therapeutic development as exemplified by the use of selective small-molecule MMP inhibitors in diabetic wound healing, spinal cord injury, stroke, traumatic brain injury, cancer metastasis, and viral infection. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman. Copyright © 2017 Elsevier B.V. All rights reserved.

Visualization of molecular structures using HoloLens-based augmented reality

PubMed Central

Hoffman, MA; Provance, JB

2017-01-01

Biological molecules and biologically active small molecules are complex three dimensional structures. Current flat screen monitors are limited in their ability to convey the full three dimensional characteristics of these molecules. Augmented reality devices, including the Microsoft HoloLens, offer an immersive platform to change how we interact with molecular visualizations. We describe a process to incorporate the three dimensional structures of small molecules and complex proteins into the Microsoft HoloLens using aspirin and the human leukocyte antigen (HLA) as examples. Small molecular structures can be introduced into the HoloStudio application, which provides native support for rotating, resizing and performing other interactions with these molecules. Larger molecules can be imported through the Unity gaming development platform and then Microsoft Visual Developer. The processes described here can be modified to import a wide variety of molecular structures into augmented reality systems and improve our comprehension of complex structural features. PMID:28815109

Adrenocortical Gap Junctions and Their Functions

PubMed Central

Bell, Cheryl L.; Murray, Sandra A.

2016-01-01

Adrenal cortical steroidogenesis and proliferation are thought to be modulated by gap junction-mediated direct cell–cell communication of regulatory molecules between cells. Such communication is regulated by the number of gap junction channels between contacting cells, the rate at which information flows between these channels, and the rate of channel turnover. Knowledge of the factors regulating gap junction-mediated communication and the turnover process are critical to an understanding of adrenal cortical cell functions, including development, hormonal response to adrenocorticotropin, and neoplastic dedifferentiation. Here, we review what is known about gap junctions in the adrenal gland, with particular attention to their role in adrenocortical cell steroidogenesis and proliferation. Information and insight gained from electrophysiological, molecular biological, and imaging (immunocytochemical, freeze fracture, transmission electron microscopic, and live cell) techniques will be provided. PMID:27445985

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294

Metathesis depolymerizable surfactants

DOEpatents

Jamison, Gregory M [Albuquerque, NM; Wheeler, David R [Albuquerque, NM; Loy, Douglas A [Tucson, AZ; Simmons, Blake A [San Francisco, CA; Long, Timothy M [Evanston, IL; McElhanon, James R [Manteca, CA; Rahimian, Kamyar [Albuquerque, NM; Staiger, Chad L [Albuquerque, NM

2008-04-15

A class of surfactant molecules whose structure includes regularly spaced unsaturation in the tail group and thus, can be readily decomposed by ring-closing metathesis, and particularly by the action of a transition metal catalyst, to form small molecule products. These small molecules are designed to have increased volatility and/or enhanced solubility as compared to the original surfactant molecule and are thus easily removed by solvent extraction or vacuum extraction at low temperature. By producing easily removable decomposition products, the surfactant molecules become particularly desirable as template structures for preparing meso- and microstructural materials with tailored properties.

Numerical exploration of non-axisymmetric divertor closure in the small angle slot (SAS) divertor at DIII-D

DOE PAGES

Frerichs, H.; Schmitz, O.; Covele, B.; ...

2018-02-28

Numerical simulations of toroidal asymmetries in a tightly baffled small angle slot (SAS) divertor on the DIII-D tokamak show that toroidal asymmetries in divertor closure result in (non-axisymmetric) local onset of detachment within a density window of 10-15% on top of the nominal threshold separatrix density. The SAS divertor is explored at DIII-D for improving access to cold, dissipative/detached divertor conditions. The narrow width of the slot divertor coupled with a small magnetic field line-to-target angle facilitates the buildup of neutral density, thereby increasing radiative and neutrals-related (atoms and molecules) losses in the divertor. Therefore, small changes in the strikemore » point location can be expected to have a large impact on diverter conditions. The combination of misaligned slot structure and non-axisymmetric perturbations to the magnetic field configuration causes the strike point to move along the divertor target plate, possibly leaving the diverter slot at some locations. The latter extreme case essentially introduces an opening in the divertor slot from where recycling neutrals can easily escape, and thereby degrade the performance of the slot divertor. Such a strike point dislocation is approximated by a finite gap in the divertor baffle for which three dimensional edge plasma and neutral gas simulations are performed with the EMC3-EIRENE code.« less

Numerical exploration of non-axisymmetric divertor closure in the small angle slot (SAS) divertor at DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frerichs, H.; Schmitz, O.; Covele, B.

Numerical simulations of toroidal asymmetries in a tightly baffled small angle slot (SAS) divertor on the DIII-D tokamak show that toroidal asymmetries in divertor closure result in (non-axisymmetric) local onset of detachment within a density window of 10-15% on top of the nominal threshold separatrix density. The SAS divertor is explored at DIII-D for improving access to cold, dissipative/detached divertor conditions. The narrow width of the slot divertor coupled with a small magnetic field line-to-target angle facilitates the buildup of neutral density, thereby increasing radiative and neutrals-related (atoms and molecules) losses in the divertor. Therefore, small changes in the strikemore » point location can be expected to have a large impact on diverter conditions. The combination of misaligned slot structure and non-axisymmetric perturbations to the magnetic field configuration causes the strike point to move along the divertor target plate, possibly leaving the diverter slot at some locations. The latter extreme case essentially introduces an opening in the divertor slot from where recycling neutrals can easily escape, and thereby degrade the performance of the slot divertor. Such a strike point dislocation is approximated by a finite gap in the divertor baffle for which three dimensional edge plasma and neutral gas simulations are performed with the EMC3-EIRENE code.« less

Numerical exploration of non-axisymmetric divertor closure in the small angle slot (SAS) divertor at DIII-D

NASA Astrophysics Data System (ADS)

Frerichs, H.; Schmitz, O.; Covele, B.; Feng, Y.; Guo, H. Y.; Hill, D.

2018-05-01

Numerical simulations of toroidal asymmetries in a tightly baffled small angle slot (SAS) divertor on the DIII-D tokamak show that toroidal asymmetries in divertor closure result in (non-axisymmetric) local onset of detachment within a density window of 10-15% on top of the nominal threshold separatrix density. The SAS divertor is explored at DIII-D for improving access to cold, dissipative/detached divertor conditions. The narrow width of the slot divertor coupled with a small magnetic field line-to-target angle facilitates the buildup of neutral density, thereby increasing radiative and neutrals-related (atoms and molecules) losses in the divertor. Small changes in the strike point location can be expected to have a large impact on divertor conditions. The combination of misaligned slot structure and non-axisymmetric perturbations to the magnetic field configuration causes the strike point to move along the divertor target plate, possibly leaving the divertor slot at some locations. The latter extreme case essentially introduces an opening in the divertor slot from where recycling neutrals can easily escape, and thereby degrade the performance of the slot divertor. Such a strike point dislocation is approximated by a finite gap in the divertor baffle for which 3D edge plasma and neutral gas simulations are performed with the EMC3-EIRENE code.

Concentration-related response potentiometric titrations to study the interaction of small molecules with large biomolecules.

PubMed

Hamidi-Asl, Ezat; Daems, Devin; De Wael, Karolien; Van Camp, Guy; Nagels, Luc J

2014-12-16

In the present paper, the utility of a special potentiometric titration approach for recognition and calculation of biomolecule/small-molecule interactions is reported. This approach is fast, sensitive, reproducible, and inexpensive in comparison to the other methods for the determination of the association constant values (Ka) and the interaction energies (ΔG). The potentiometric titration measurement is based on the use of a classical polymeric membrane indicator electrode in a solution of the small-molecule ligand. The biomolecule is used as a titrant. The potential is measured versus a reference electrode and transformed into a concentration-related signal over the entire concentration interval, also at low concentrations, where the millivolt (y-axis) versus log canalyte (x-axis) potentiometric calibration curve is not linear. In the procedure, Ka is calculated for the interaction of cocaine with a cocaine binding aptamer and with an anticocaine antibody. To study the selectivity and cross-reactivity, other oligonucleotides and aptamers are tested, as well as other small ligand molecules such as tetrakis(4-chlorophenyl)borate, metergoline, lidocaine, and bromhexine. The calculated Ka compared favorably to the value reported in the literature using surface plasmon resonance. The potentiometric titration approach called "concentration-related response potentiometry" is used to study molecular interaction for seven macromolecular target molecules and four small-molecule ligands.

Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications.

PubMed

Jiang, Xiqian; Wang, Lingfei; Carroll, Shaina L; Chen, Jianwei; Wang, Meng C; Wang, Jin

2018-02-16

The concentrations of reactive oxygen/nitrogen species (ROS/RNS) are critical to various biochemical processes. Small-molecule fluorescent probes have been widely used to detect and/or quantify ROS/RNS in many redox biology studies and serve as an important complementary to protein-based sensors with unique applications. Recent Advances: New sensing reactions have emerged in probe development, allowing more selective and quantitative detection of ROS/RNS, especially in live cells. Improvements have been made in sensing reactions, fluorophores, and bioavailability of probe molecules. In this review, we will not only summarize redox-related small-molecule fluorescent probes but also lay out the challenges of designing probes to help redox biologists independently evaluate the quality of reported small-molecule fluorescent probes, especially in the chemistry literature. We specifically highlight the advantages of reversibility in sensing reactions and its applications in ratiometric probe design for quantitative measurements in living cells. In addition, we compare the advantages and disadvantages of small-molecule probes and protein-based probes. The low physiological relevant concentrations of most ROS/RNS call for new sensing reactions with better selectivity, kinetics, and reversibility; fluorophores with high quantum yield, wide wavelength coverage, and Stokes shifts; and structural design with good aqueous solubility, membrane permeability, low protein interference, and organelle specificity. Antioxid. Redox Signal. 00, 000-000.

Design strategy for photoinduced electron transfer-based small-molecule fluorescent probes of biomacromolecules.

PubMed

Zhang, Wei; Ma, Zhao; Du, Lupei; Li, Minyong

2014-06-07

As the cardinal support of innumerable biological processes, biomacromolecules such as proteins, nucleic acids and polysaccharides are of importance to living systems. The key to understanding biological processes is to realize the role of these biomacromolecules in thte localization, distribution, conformation and interaction with other molecules. With the current development and adaptation of fluorescent technologies in biomedical and pharmaceutical fields, the fluorescence imaging (FLI) approach of using small-molecule fluorescent probes is becoming an up-to-the-minute method for the detection and monitoring of these imperative biomolecules in life sciences. However, conventional small-molecule fluorescent probes may provide undesirable results because of their intrinsic deficiencies such as low signal-to-noise ratio (SNR) and false-positive errors. Recently, small-molecule fluorescent probes with a photoinduced electron transfer (PET) "on/off" switch for biomacromolecules have been thoroughly considered. When recognized by the biomacromolecules, these probes turn on/off the PET switch and change the fluorescence intensity to present a high SNR result. It should be emphasized that these PET-based fluorescent probes could be advantageous for understanding the pathogenesis of various diseases caused by abnormal expression of biomacromolecules. The discussion of this successful strategy involved in this review will be a valuable guide for the further development of new PET-based small-molecule fluorescent probes for biomacromolecules.

Inhibition of HIF-2.alpha. heterodimerization with HIF1.beta. (ARNT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruick, Richard K.; Caldwell, Charles G.; Frantz, Doug E.

2017-09-12

Provided is a method of inhibiting heterodimerization of HIF-2.alpha. to HIF1.beta. (ARNT) comprising binding certain small molecules to the HIF-2.alpha. PAS-B domain cavity but not to HIF1.alpha. and inhibiting HIF-2.alpha. heterodimerization to HIF1.beta. (ARNT) but not inhibiting HIF1.alpha. heterodimerization to HIF1.beta. (ARNT). Those certain small molecules are also referenced synonymously as HIF2-HDI and HIF2.alpha. heterodimerization inhibitors and also simply as certain small molecules.

Fullerene-free small molecule organic solar cells with a high open circuit voltage of 1.15 V.

PubMed

Ni, Wang; Li, Miaomiao; Kan, Bin; Liu, Feng; Wan, Xiangjian; Zhang, Qian; Zhang, Hongtao; Russell, Thomas P; Chen, Yongsheng

2016-01-11

A new small molecule named DTBTF with thiobarbituric acid as a terminal group was designed and synthesized as an acceptor for organic photovoltaic applications. DTBTF exhibits strong absorption in the visible region, and a relatively high lying LUMO energy level (-3.62 eV). All-small-molecule organic solar cells based on DR3TSBDT:DTBTF blend films show a considerable PCE of 3.84% with a high V(oc) of 1.15 V.

Expression and Function of Connexin 43 in Human Gingival Wound Healing and Fibroblasts

PubMed Central

Tarzemany, Rana; Jiang, Guoqiao; Larjava, Hannu; Häkkinen, Lari

2015-01-01

Connexins (C×s) are a family of transmembrane proteins that form hemichannels and gap junctions (GJs) on the cell membranes, and transfer small signaling molecules between the cytoplasm and extracellular space and between connecting cells, respectively. Among C×s, suppressing C×43 expression or function promotes skin wound closure and granulation tissue formation, and may alleviate scarring, but the mechanisms are not well understood. Oral mucosal gingiva is characterized by faster wound closure and scarless wound healing outcome as compared to skin wounds. Therefore, we hypothesized that C×43 function is down regulated during human gingival wound healing, which in fibroblasts promotes expression of genes conducive for fast and scarless wound healing. Cultured gingival fibroblasts expressed C×43 as their major connexin. Immunostaining of unwounded human gingiva showed that C×43 was abundantly present in the epithelium, and in connective tissue formed large C×43 plaques in fibroblasts. At the early stages of wound healing, C×43 was strongly down regulated in wound epithelial cells and fibroblasts, returning to the level of normal tissue by day 60 post-wounding. Blocking of C×43 function by C×43 mimetic peptide Gap27 suppressed GJ-mediated dye transfer, promoted migration, and caused significant changes in the expression of wound healing-associated genes in gingival fibroblasts. In particular, out of 54 genes analyzed, several MMPs and TGF-β1, involved in regulation of inflammation and extracellular matrix (ECM) turnover, and VEGF-A, involved in angiogenesis, were significantly upregulated while pro-fibrotic ECM molecules, including Collagen type I, and cell contractility-related molecules were significantly down regulated. These responses involved MAPK, GSK3α/β and TGF-β signaling pathways, and AP1 and SP1 transcription factors. Thus, suppressed function of C×43 in fibroblasts promotes their migration, and regulates expression of wound healing-associated genes via AP1, SP1, MAPK, GSK3α/β and TGF-β signaling pathways, and may promote fast and scarless wound healing in human gingiva. PMID:25584940

Molecular Engineering Strategy for High Efficiency Fullerene-Free Organic Solar Cells Using Conjugated 1,8-Naphthalimide and Fluorenone Building Blocks.

PubMed

Do, Thu Trang; Pham, Hong Duc; Manzhos, Sergei; Bell, John M; Sonar, Prashant

2017-05-24

We designed, synthesized, and characterized a series of novel electron deficient small molecule nonfullerene acceptors based on 1,8-naphthalimide (NAI) and 9-fluorenone (FN) with different branched alkyl chains using various techniques. These molecules are based on an acceptor-donor-acceptor-donor-acceptor (A1-D-A2-D-A1) molecular design configuration with NAI as the end-capping acceptor (A1), FN as electron-withdrawing central (A2) group, and thiophene ring as a donor (D) unit. These materials are named as NAI-FN-NAI (BO) and NAI-FN-NAI (HD) where BO and HD represent butyloctyl and hexyldecyl alkyl groups, respectively. To further modify energy levels of these materials, we converted the weak electron withdrawing ketonic group (C═O) attached to the FN moiety of NAI-FN-NAI (BO) to a stronger electron withdrawing cyano group (C≡N) to obtain the compound NAI-FCN-NAI (BO) by keeping the same alkyl chain. The optical, electrochemical, and thermal properties of the new acceptors were studied. The materials exhibited higher to medium band gaps, low lowest unoccupied molecular orbital (LUMO) energy levels, and highly thermally stable properties. Organic solar cell devices employing conventional poly(3-hexylthiophene) (P3HT) a donor polymer and the newly designed small molecules as the acceptor were investigated. Among all new materials, organic solar cell devices based on NAI-FN-NAI (BO) as an acceptor exhibit the highest performance with an open circuit voltage (V OC ) of 0.88 V, a short-circuit current density (J SC ) of 9.1 mAcm -2 , a fill factor (FF) of 45%, and an overall power conversion efficiency (PCE) of 3.6%. This is the first report of 9-fluorenone based nonfullerene acceptor with P3HT donor in organic solar cell devices with such a promising performance.

Spontaneous emission near the edge of a photonic band gap

NASA Astrophysics Data System (ADS)

John, Sajeev; Quang, Tran

1994-08-01

The spectral and dynamical features of spontaneous emission from two and three-level atoms in which one transition frequency lay near the edge of a photonic band gap (PBG) were derived. These features included temporal oscillations, fractionalized steady-state atomic population on the excited state, spectral splitting and subnatural bandwidth. The effect of N-1 unexcited atoms were also taken into account. The direct consequences of photon localization as embodied in the photon-atom bound state were observed. One feasible experimental accomplishment of these effects may ensue from laser-cooled atoms in the void regions of a PBG medium. Another option is the application of an organic impurity molecule such as pentacene. Such molecules were known to show extremely narrow linewidths when placed in fitting solid hosts.

Electron and Cooper-pair transport across a single magnetic molecule explored with a scanning tunneling microscope

NASA Astrophysics Data System (ADS)

Brand, J.; Gozdzik, S.; Néel, N.; Lado, J. L.; Fernández-Rossier, J.; Kröger, J.

2018-05-01

A scanning tunneling microscope is used to explore the evolution of electron and Cooper-pair transport across single Mn-phthalocyanine molecules adsorbed on Pb(111) from tunneling to contact ranges. Normal-metal as well as superconducting tips give rise to a gradual transition of the Bardeen-Cooper-Schrieffer energy gap in the tunneling range into a zero-energy resonance close to and at contact. Supporting transport calculations show that in the normal-metal-superconductor junctions this resonance reflects the merging of in-gap Yu-Shiba-Rusinov states as well as the onset of Andreev reflection. For the superconductor-superconductor contacts, the zero-energy resonance is rationalized in terms of a finite Josephson current that is carried by phase-dependent Andreev and Yu-Shiba-Rusinov levels.

Tuned range separated hybrid functionals for solvated low bandgap oligomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan

2015-07-21

The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is tomore » use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.« less

Effect of interstitial palladium on plasmon-driven charge transfer in nanoparticle dimers.

PubMed

Lerch, Sarah; Reinhard, Björn M

2018-04-23

Capacitive plasmon coupling between noble metal nanoparticles (NPs) is characterized by an increasing red-shift of the bonding dipolar plasmon mode (BDP) in the classical electromagnetic coupling regime. This model breaks down at short separations where plasmon-driven charge transfer induces a gap current between the NPs with a magnitude and separation dependence that can be modulated if molecules are present in the gap. Here, we use gap contained DNA as a scaffold for the growth of palladium (Pd) NPs in the gap between two gold NPs and investigate the effect of increasing Pd NP concentration on the BDP mode. Consistent with enhanced plasmon-driven charge transfer, the integration of discrete Pd NPs depolarizes the capacitive BDP mode over longer interparticle separations than is possible in only DNA-linked Au NPs. High Pd NP densities in the gap increases the gap conductance and induces the transition from capacitive to conductive coupling.

STM study of C60F18 high dipole moment molecules on Au(111)

NASA Astrophysics Data System (ADS)

Bairagi, K.; Bellec, A.; Chumakov, R. G.; Menshikov, K. A.; Lagoute, J.; Chacon, C.; Girard, Y.; Rousset, S.; Repain, V.; Lebedev, A. M.; Sukhanov, L. P.; Svechnikov, N. Yu.; Stankevich, V. G.

2015-11-01

Scanning tunneling microscopy and spectroscopy studies of C60F18 molecules deposited on Au(111) are reported and compared to C60 molecules both at liquid helium temperature and room temperature (RT). Whereas adsorption and electronic properties of C60F18 single molecules were studied at low temperature (LT), self-assemblies were investigated at RT. In both cases, the fluorine atoms of the C60F18 molecules are pointed towards the surface. Individual C60F18 molecules on Au(111) have a HOMO-LUMO gap of 2.9 eV. The self-assembled islands exhibit a close-packed hexagonal lattice with amorphous borders. The comparison with C60 molecules clearly demonstrates the influence of the C60F18 electric dipole moment (EDM) on the electronic properties of single molecules and on the thermodynamics of self-assembled islands. Besides, the apparent height value of a separate molecule increases in a self-assembly environment as a result of a depolarization phenomenon.

A size selective porous silicon grating-coupled Bloch surface and sub-surface wave biosensor.

PubMed

Rodriguez, Gilberto A; Ryckman, Judson D; Jiao, Yang; Weiss, Sharon M

2014-03-15

A porous silicon (PSi) grating-coupled Bloch surface and sub-surface wave (BSW/BSSW) biosensor is demonstrated to size selectively detect the presence of both large and small molecules. The BSW is used to sense large immobilized analytes at the surface of the structure while the BSSW that is confined inside but near the top of the structure is used to sensitively detect small molecules. Functionality of the BSW and BSSW modes is theoretically described by dispersion relations, field confinements, and simulated refractive index shifts within the structure. The theoretical results are experimentally verified by detecting two different small chemical molecules and one large 40 base DNA oligonucleotide. The PSi-BSW/BSSW structure is benchmarked against current porous silicon technology and is shown to have a 6-fold higher sensitivity in detecting large molecules and a 33% improvement in detecting small molecules. This is the first report of a grating-coupled BSW biosensor and the first report of a BSSW propagating mode. © 2013 Published by Elsevier B.V.

[Innovative application of small molecules to influence -pathogenicity of dental plaque].

PubMed

Janus, M M; Volgenant, C M C; Krom, B P

2018-05-01

Current preventive measures against infectious oral diseases are mainly focussed on plaque removal and promoting a healthy lifestyle. This in vitro study investigated a third preventive method: maintaining healthy dental plaque with the use of small molecules. As a model of dental plaque, in vitro biofilms were cultivated under conditions that induce pathogenic characteristics. The effect of erythritol and other small molecules on the pathogenic characteristics and bacterial composition of the biofilm was evaluated. The artificial sweetener erythritol and the molecule 3-Oxo-N-(2-oxycyclohexyl)dodecanamide (3-Oxo-N) had no clinically relevant effect on total biofilm formation. Erythritol did, however, lower the gingivitis related protease activity of the biofilm, while 3-Oxo-N blocked the caries related lactic acid accumulation. Furthermore, both substances ensured the biofilm maintained a young, non-pathogenic microbial composition. This shows it is possible to influence the dental plaque in a positive manner in vitro with the help of small molecules. Further research is necessary before this manipulation of dental plaque can be applied.

Testing glueline continuity in standard-size hardwood blanks by mechanical methods

Treesearch

David W. Patterson; Nathan D. Hesterman; Charles Gatchell

1991-01-01

Glueline continuity is very critical in standard-size hardwood blanks because the blanks are cut up into small furniture parts, and a small gap in the glueline of a blank may extend across the whole part—or a gap may appear as a crack in the final product. Strength is not a critical factor. The objective of this study was to determine if a gap in a glueline can be...

A Prospective Method to Guide Small Molecule Drug Design

ERIC Educational Resources Information Center

Johnson, Alan T.

2015-01-01

At present, small molecule drug design follows a retrospective path when considering what analogs are to be made around a current hit or lead molecule with the focus often on identifying a compound with higher intrinsic potency. What this approach overlooks is the simultaneous need to also improve the physicochemical (PC) and pharmacokinetic (PK)…

Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

NASA Astrophysics Data System (ADS)

Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

2018-03-01

Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ˜0.1 s-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase.

PubMed

Wang, Quan; Serban, Andrew J; Wachter, Rebekka M; Moerner, W E

2018-03-28

Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ∼0.1 s -1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

Comparative dynamics of small mammal populations in treefall gaps and surrounding understorey within Amazonian rainforest

USGS Publications Warehouse

Beck, H.; Gaines, M.S.; Hines, J.E.; Nichols, J.D.

2004-01-01

Variation in food resource availability can have profound effects on habitat selection and dynamics of populations. Previous studies reported higher food resource availability and fruit removal in treefall gaps than in the understorey. Therefore, gaps have been considered 'keystone habitat' for Neotropical frugivore birds. Here we test if this prediction would also hold for terrestrial small mammals. In the Amazon, we quantified food resource availability in eleven treefall gaps and paired understorey habitats and used feeding experiments to test if two common terrestrial rodents (Oryzomys megacephalus and Proechimys spp.) would perceive differences between habitats. We live-trapped small mammals in eleven gaps and understorey sites for two years, and compared abundance, fitness components (survival and per capita recruitment) and dispersal of these two rodent species across gaps and understorey and seasons (rainy and dry). Our data indicated no differences in resource availability and consumption rate between habitats. Treefall gaps may represent a sink habitat for Oryzomys where individuals had lower fitness, apparently because of habitat-specific ant predation on early life stages, than in the understorey, the source habitat. Conversely, gaps may be source habitat for Proechimys where individuals had higher fitness, than in the understorey, the sink habitat. Our results suggest the presence of source-sink dynamics in a tropical gap-understorey landscape, where two rodent species perceive habitats differently. This may be a mechanism for their coexistence in a heterogeneous and species-diverse system.

Nonstandard convergence to jamming in random sequential adsorption: The case of patterned one-dimensional substrates

NASA Astrophysics Data System (ADS)

Verma, Arjun; Privman, Vladimir

2018-02-01

We study approach to the large-time jammed state of the deposited particles in the model of random sequential adsorption. The convergence laws are usually derived from the argument of Pomeau which includes the assumption of the dominance, at large enough times, of small landing regions into each of which only a single particle can be deposited without overlapping earlier deposited particles and which, after a certain time are no longer created by depositions in larger gaps. The second assumption has been that the size distribution of gaps open for particle-center landing in this large-time small-gaps regime is finite in the limit of zero gap size. We report numerical Monte Carlo studies of a recently introduced model of random sequential adsorption on patterned one-dimensional substrates that suggest that the second assumption must be generalized. We argue that a region exists in the parameter space of the studied model in which the gap-size distribution in the Pomeau large-time regime actually linearly vanishes at zero gap sizes. In another region, the distribution develops a threshold property, i.e., there are no small gaps below a certain gap size. We discuss the implications of these findings for new asymptotic power-law and exponential-modified-by-a-power-law convergences to jamming in irreversible one-dimensional deposition.

Electrical transmission between mammalian neurons is supported by a small fraction of gap junction channels.

PubMed

Curti, Sebastian; Hoge, Gregory; Nagy, James I; Pereda, Alberto E

2012-06-01

Electrical synapses formed by gap junctions between neurons create networks of electrically coupled neurons in the mammalian brain, where these networks have been found to play important functional roles. In most cases, interneuronal gap junctions occur at remote dendro-dendritic contacts, making difficult accurate characterization of their physiological properties and correlation of these properties with their anatomical and morphological features of the gap junctions. In the mesencephalic trigeminal (MesV) nucleus where neurons are readily accessible for paired electrophysiological recordings in brain stem slices, our recent data indicate that electrical transmission between MesV neurons is mediated by connexin36 (Cx36)-containing gap junctions located at somato-somatic contacts. We here review evidence indicating that electrical transmission between these neurons is supported by a very small fraction of the gap junction channels present at cell-cell contacts. Acquisition of this evidence was enabled by the unprecedented experimental access of electrical synapses between MesV neurons, which allowed estimation of the average number of open channels mediating electrical coupling in relation to the average number of gap junction channels present at these contacts. Our results indicate that only a small proportion of channels (~0.1 %) appear to be conductive. On the basis of similarities with other preparations, we postulate that this phenomenon might constitute a general property of vertebrate electrical synapses, reflecting essential aspects of gap junction function and maintenance.

Demonstration of sub-femtomole sensitivity for small molecules with microsphere ring resonator sensors

NASA Astrophysics Data System (ADS)

White, Ian M.; Oveys, Hesam; Fan, Xudong

2006-02-01

Optical microsphere resonators can function as highly sensitive bio/chemical sensors due to the large Q-factor, which leads to high light-matter interaction. The whispering gallery modes (WGM) arise at the surface of the microsphere, creating a highly enhanced optical field that interacts with matter on or near the microsphere surface. As a result, the spectral position of the WGM is extremely sensitive to refractive index changes near the surface, such as when bio/chemical molecules bind to the sphere. We show the potential feasibility of a microsphere ring resonator as a sensor for small molecules by demonstrating detection of sub-femtomole changes in SiO II molecules at the surface of the microsphere. In this experiment, the silica molecules act as an excellent model for small molecule analytes because of their 60 Dalton molecular weight, and because we know nearly the exact quantity of molecules at the surface, which enables a sensitivity characterization. We measure the spectral shifts in the WGMs when low concentrations of hydrofluoric acid (HF) are added to a solution that is being probed by the microsphere. As the HF molecules break apart the SiO II molecules at the sphere surface, the WGMs shift due to the sub-nano-scale decrease in the size of the microsphere. These calculations show that the sensitivity of this microsphere resonator is on the order of 500 attomoles. Our results will lead to the utilization of optical microspheres for detection of trace quantities of small molecules for such applications as drug discovery, environmental monitoring, and enzyme detection using peptide cleavage.

[Microclimate dynamics of pit and mound complex within different sizes of forest gaps in Pinus koraiensis-dominated broadleaved mixed forest].

PubMed

Wei, Quan-Shuai; Wang, Jing-Hua; Duan, Wen-Biao; Chen, Li-Xin; Wang, Ting; Han, Dong-Hui; Gu, Wei

2014-03-01

An investigation was conducted in a 2.25 hm2 plot of Pinus koraiensis-dominated broad-leaved mixed forest to study basic characteristics of 7 small gaps, 5 middle gaps, 3 large gaps and 7 closed stands within 38 pit and mound complexes caused by treefall in May 2012. From June to September 2012, the soil temperature, soil water content and relative humidity at five microsites (pit bottom, pit wall, mound top, mound face and undisturbed closed stands) were measured in six sunny days each month. The results showed that among the five microsites in every month, the mound top had the highest soil temperature and the lowest water content and relative humidity, and vice versa for the pit bottom. Mostly, the differences in the above indicators among the five microsites were significant. From June to September, the mean soil temperatures for all microsites at pit and mound complex in the various gaps and closed stands were in the order of large gap>middle gap >small gap>closed stand; but the soil water content ranked differently every month. In June, August and September, the mean relative humidities for all microsites in the various gaps and closed stands were in the order of closed stand>small gap>middle gap>large gap. Mostly, the differences in the above indicators between all microsites in the various gaps and closed stand were significant. The mean monthly soil temperature and relative humidity were highest in July, but lowest in September. The maximal mean monthly soil water content occurred in July and the minimal one in September for each microsite except the undisturbed closed stands, where the maximal mean monthly soil water content occurred in July. The variation of the microclimate at the pit and mound complex was mainly influenced by gap size, microsite, and time.

Saturation recovery EPR and ELDOR at W-band for spin labels

PubMed Central

Froncisz, Wojciech; Camenisch, Theodore G.; Ratke, Joseph J.; Anderson, James R.; Subczynski, Witold K.; Strangeway, Robert A.; Sidabras, Jason W.; Hyde, James S.

2008-01-01

A reference-arm W-band (94 GHz) microwave bridge with two sample-irradiation arms for saturation recovery (SR) EPR and ELDOR experiments is described. Frequencies in each arm are derived from 2 GHz synthesizers that have a common time-base and are translated to 94 GHz in steps of 33 and 59 GHz. Intended applications are to nitroxide radical spin labels and spin probes in the liquid phase. An enabling technology is the use of a W-band loop-gap resonator (LGR) (J.W. Sidabras et al., Rev. Sci. Instrum. 78 (2007) 034701). The high efficiency parameter (8.2 GW−1/2 with sample) permits the saturating pump pulse level to be just 5 mW or less. Applications of SR EPR and ELDOR to the hydrophilic spin labels 3-carbamoyl-2,2,5,5-tetra-methyl-3-pyrroline-1-yloxyl (CTPO) and 2,2,6,6,-tetramethyl-4-piperidone-1-oxyl (TEMPONE) are described in detail. In the SR ELDOR experiment, nitrogen nuclear relaxation as well as Heisenberg exchange transfer saturation from pumped to observed hyperfine transitions. SR ELDOR was found to be an essential method for measurements of saturation transfer rates for small molecules such as TEMPONE. Free induction decay (FID) signals for small nitroxides at W-band are also reported. Results are compared with multifrequency measurements of T1e previously reported for these molecules in the range of 2 to 35 GHz (J.S. Hyde et al., J. Phys. Chem. B 108 (2004) 9524–9529). The values of T1e decrease at 94 GHz relative to values at 35 GHz. PMID:18547848

Small Molecule Targeted Recruitment of a Nuclease to RNA.

PubMed

Costales, Matthew G; Matsumoto, Yasumasa; Velagapudi, Sai Pradeep; Disney, Matthew D

2018-06-06

The choreography between RNA synthesis and degradation is a key determinant in biology. Engineered systems such as CRISPR have been developed to rid a cell of RNAs. Here, we show that a small molecule can recruit a nuclease to a specific transcript, triggering its destruction. A small molecule that selectively binds the oncogenic microRNA(miR)-96 hairpin precursor was appended with a short 2'-5' poly(A) oligonucleotide. The conjugate locally activated endogenous, latent ribonuclease (RNase L), which selectively cleaved the miR-96 precursor in cancer cells in a catalytic and sub-stoichiometric fashion. Silencing miR-96 derepressed pro-apoptotic FOXO1 transcription factor, triggering apoptosis in breast cancer, but not healthy breast, cells. These results demonstrate that small molecules can be programmed to selectively cleave RNA via nuclease recruitment and has broad implications.

Small-molecule control of protein function through Staudinger reduction

NASA Astrophysics Data System (ADS)

Luo, Ji; Liu, Qingyang; Morihiro, Kunihiko; Deiters, Alexander

2016-11-01

Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small-molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl transfer RNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small-molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (enhanced green fluorescent protein), protein translocation (nuclear localization sequence), DNA recombination (Cre) and gene editing (Cas9).

RISC-Target Interaction: Cleavage and Translational Suppression

PubMed Central

van den Berg, Arjen; Mols, Johann; Han, Jiahuai

2008-01-01

Summary Small RNA molecules have been known and utilized to suppress gene expression for more than a decade. The discovery that these small RNA molecules are endogenously expressed in many organisms and have a critical role in controlling gene expression have led to the arising of a whole new field of research. Termed small interfering RNA (siRNA) or microRNA (miRNA) these ~22 nt RNA molecules have the capability to suppress gene expression through various mechanisms once they are incorporated in the multi-protein RNA-Induced Silencing Complex (RISC) and interact with their target mRNA. This review introduces siRNAs and microRNAs in a historical perspective and focuses on the key molecules in RISC, structural properties and mechanisms underlying the process of small RNA regulated post-transcriptional suppression of gene expression. PMID:18692607

Inkjet-Printed Small-Molecule Organic Light-Emitting Diodes: Halogen-Free Inks, Printing Optimization, and Large-Area Patterning.

PubMed

Zhou, Lu; Yang, Lei; Yu, Mengjie; Jiang, Yi; Liu, Cheng-Fang; Lai, Wen-Yong; Huang, Wei

2017-11-22

Manufacturing small-molecule organic light-emitting diodes (OLEDs) via inkjet printing is rather attractive for realizing high-efficiency and long-life-span devices, yet it is challenging. In this paper, we present our efforts on systematical investigation and optimization of the ink properties and the printing process to enable facile inkjet printing of conjugated light-emitting small molecules. Various factors on influencing the inkjet-printed film quality during the droplet generation, the ink spreading on the substrates, and its solidification processes have been systematically investigated and optimized. Consequently, halogen-free inks have been developed and large-area patterning inkjet printing on flexible substrates with efficient blue emission has been successfully demonstrated. Moreover, OLEDs manufactured by inkjet printing the light-emitting small molecules manifested superior performance as compared with their corresponding spin-cast counterparts.

Biased and unbiased strategies to identify biologically active small molecules.

PubMed

Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

2014-08-15

Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. Copyright © 2014. Published by Elsevier Ltd.

Screening small-molecule compound microarrays for protein ligands without fluorescence labeling with a high-throughput scanning microscope.

PubMed

Fei, Yiyan; Landry, James P; Sun, Yungshin; Zhu, Xiangdong; Wang, Xiaobing; Luo, Juntao; Wu, Chun-Yi; Lam, Kit S

2010-01-01

We describe a high-throughput scanning optical microscope for detecting small-molecule compound microarrays on functionalized glass slides. It is based on measurements of oblique-incidence reflectivity difference and employs a combination of a y-scan galvometer mirror and an x-scan translation stage with an effective field of view of 2 cm x 4 cm. Such a field of view can accommodate a printed small-molecule compound microarray with as many as 10,000 to 20,000 targets. The scanning microscope is capable of measuring kinetics as well as endpoints of protein-ligand reactions simultaneously. We present the experimental results on solution-phase protein reactions with small-molecule compound microarrays synthesized from one-bead, one-compound combinatorial chemistry and immobilized on a streptavidin-functionalized glass slide.

Screening small-molecule compound microarrays for protein ligands without fluorescence labeling with a high-throughput scanning microscope

PubMed Central

Fei, Yiyan; Landry, James P.; Sun, Yungshin; Zhu, Xiangdong; Wang, Xiaobing; Luo, Juntao; Wu, Chun-Yi; Lam, Kit S.

2010-01-01

We describe a high-throughput scanning optical microscope for detecting small-molecule compound microarrays on functionalized glass slides. It is based on measurements of oblique-incidence reflectivity difference and employs a combination of a y-scan galvometer mirror and an x-scan translation stage with an effective field of view of 2 cm×4 cm. Such a field of view can accommodate a printed small-molecule compound microarray with as many as 10,000 to 20,000 targets. The scanning microscope is capable of measuring kinetics as well as endpoints of protein-ligand reactions simultaneously. We present the experimental results on solution-phase protein reactions with small-molecule compound microarrays synthesized from one-bead, one-compound combinatorial chemistry and immobilized on a streptavidin-functionalized glass slide. PMID:20210464

Synthetic Small Molecule Inhibitors of Hh Signaling As Anti-Cancer Chemotherapeutics

PubMed Central

Maschinot, C.A.; Pace, J.R.; Hadden, M.K.

2016-01-01

The hedgehog (Hh) pathway is a developmental signaling pathway that is essential to the proper embryonic development of many vertebrate systems. Dysregulation of Hh signaling has been implicated as a causative factor in the development and progression of several forms of human cancer. As such, the development of small molecule inhibitors of Hh signaling as potential anti-cancer chemotherapeutics has been a major area of research interest in both academics and industry over the past ten years. Through these efforts, synthetic small molecules that target multiple components of the Hh pathway have been identified and advanced to preclinical or clinical development. The goal of this review is to provide an update on the current status of several synthetic small molecule Hh pathway inhibitors and explore the potential of several recently disclosed inhibitory scaffolds. PMID:26310919

Fluorescence enhancement and strong-coupling in faceted plasmonic nanocavities

NASA Astrophysics Data System (ADS)

Kongsuwan, Nuttawut; Demetriadou, Angela; Chikkaraddy, Rohit; Baumberg, Jeremy J.; Hess, Ortwin

2018-06-01

Emission properties of a quantum emitter can be significantly modified inside nanometre-sized gaps between two plasmonic nanostructures. This forms a nanoscopic optical cavity which allows single-molecule detection and single-molecule strong-coupling at room temperature. However, plasmonic resonances of a plasmonic nanocavity are highly sensitive to the exact gap morphology. In this article, we shed light on the effect of gap morphology on the plasmonic resonances of a faceted nanoparticle-on-mirror (NPoM) nanocavity and their interaction with quantum emitters. We find that with increasing facet width the NPoM nanocavity provides weaker field enhancement and thus less coupling strength to a single quantum emitter since the effective mode volume increases with the facet width. However, if multiple emitters are present, a faceted NPoM nanocavity is capable of accommodating a larger number of emitters, and hence the overall coupling strength is larger due to the collective and coherent energy exchange from all the emitters. Our findings pave the way to more efficient designs of nanocavities for room-temperature light-matter strong-coupling, thus providing a big step forward to a non-cryogenic platform for quantum technologies.

Dye adsorbates BrPDI, BrGly, and BrAsp on anatase TiO2(001) for dye-sensitized solar cell applications

NASA Astrophysics Data System (ADS)

Çakır, D.; Gülseren, O.; Mete, E.; Ellialtıoǧlu, Ş.

2009-07-01

Using the first-principles plane-wave pseudopotential method within density functional theory, we systematically investigated the interaction of perylenediimide (PDI)-based dye compounds (BrPDI, BrGly, and BrAsp) with both unreconstructed (UR) and reconstructed (RC) anatase TiO2(001) surfaces. All dye molecules form strong chemical bonds with surface in the most favorable adsorption structures. In UR-BrGly, RC-BrGly, and RC-BrAsp cases, we have observed that highest occupied molecular orbital and lowest unoccupied molecular orbital levels of molecules appear within band gap and conduction-band region, respectively. Moreover, we have obtained a gap narrowing upon adsorption of BrPDI on the RC surface. Because of the reduction in effective band gap of surface-dye system and possibly achieving the visible-light activity, these results are valuable for photovoltaic and photocatalytic applications. We have also considered the effects of hydration of surface to the binding of BrPDI. It has been found that the binding energy drops significantly for the completely hydrated surfaces.

Understanding band gaps of solids in generalized Kohn-Sham theory.

PubMed

Perdew, John P; Yang, Weitao; Burke, Kieron; Yang, Zenghui; Gross, Eberhard K U; Scheffler, Matthias; Scuseria, Gustavo E; Henderson, Thomas M; Zhang, Igor Ying; Ruzsinszky, Adrienn; Peng, Haowei; Sun, Jianwei; Trushin, Egor; Görling, Andreas

2017-03-14

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn-Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations.

Understanding band gaps of solids in generalized Kohn–Sham theory

PubMed Central

Perdew, John P.; Yang, Weitao; Burke, Kieron; Yang, Zenghui; Gross, Eberhard K. U.; Scheffler, Matthias; Scuseria, Gustavo E.; Henderson, Thomas M.; Zhang, Igor Ying; Ruzsinszky, Adrienn; Peng, Haowei; Sun, Jianwei; Trushin, Egor; Görling, Andreas

2017-01-01

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn–Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations. PMID:28265085

New Small Molecule Agonists to the Thyrotropin Receptor

PubMed Central

Ali, M. Rejwan; Ma, Risheng; David, Martine; Morshed, Syed A.; Ohlmeyer, Michael; Felsenfeld, Dan P.; Lau, Zerlina; Mezei, Mihaly; Davies, Terry F.

2015-01-01

Background Novel small molecular ligands (SMLs) to the thyrotropin receptor (TSHR) have potential as improved molecular probes and as therapeutic agents for the treatment of thyroid dysfunction and thyroid cancer. Methods To identify novel SMLs to the TSHR, we developed a transcription-based luciferase-cAMP high-throughput screening system and we screened 48,224 compounds from a 100K library in duplicate. Results We obtained 62 hits using the cut-off criteria of the mean±three standard deviations above the baseline. Twenty molecules with the greatest activity were rescreened against the parent CHO-luciferase cell for nonspecific activation, and we selected two molecules (MS437 and MS438) with the highest potency for further study. These lead molecules demonstrated no detectible cross-reactivity with homologous receptors when tested against luteinizing hormone (LH)/human chorionic gonadotropin receptor and follicle stimulating hormone receptor–expressing cells. Molecule MS437 had a TSHR-stimulating potency with an EC50 of 13×10−8 M, and molecule MS438 had an EC50 of 5.3×10−8 M. The ability of these small molecule agonists to bind to the transmembrane domain of the receptor and initiate signal transduction was suggested by their activation of a chimeric receptor consisting of an LHR ectodomain and a TSHR transmembrane. Molecular modeling demonstrated that these molecules bound to residues S505 and E506 for MS438 and T501 for MS437 in the intrahelical region of transmembrane helix 3. We also examined the G protein activating ability of these molecules using CHO cells co-expressing TSHRs transfected with luciferase reporter vectors in order to measure Gsα, Gβγ, Gαq, and Gα12 activation quantitatively. The MS437 and MS438 molecules showed potent activation of Gsα, Gαq, and Gα12 similar to TSH, but neither the small molecule agonists nor TSH showed activation of the Gβγ pathway. The small molecules MS437 and MS438 also showed upregulation of thyroglobulin (Tg), sodium iodine symporter (NIS), and TSHR gene expression. Conclusions Pharmacokinetic analysis of MS437 and MS438 indicated their pharmacotherapeutic potential, and their intraperitoneal administration to normal female mice resulted in significantly increased serum thyroxine levels, which could be maintained by repeated treatments. These molecules can therefore serve as lead molecules for further development of powerful TSH agonists. PMID:25333622

Targeting RNA in mammalian systems with small molecules.

PubMed

Donlic, Anita; Hargrove, Amanda E

2018-05-03

The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease. © 2018 Wiley Periodicals, Inc.

Improving Photoconductance of Fluorinated Donors with Fluorinated Acceptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garner, Logan E.; Larson, Bryon; Oosterhout, Stefan

2016-11-21

This work investigates the influence of fluorination of both donor and acceptor materials on the generation of free charge carriers in small molecule donor/fullerene acceptor BHJ OPV active layers. A fluorinated and non-fluorinated small molecule analogue were synthesized and their optoelectronic properties characterized. The intrinsic photoconductance of blends of these small molecule donors was investigated using time-resolved microwave conductivity. Blends of the two donor molecules with a traditional non-fluorinated fullerene (PC70BM) as well as a fluorinated fullerene (C60(CF3)2-1) were investigated using 5% and 50% fullerene loading. We demonstrate for the first time that photoconductance in a 50:50 donor:acceptor BHJ blendmore » using a fluorinated fullerene can actually be improved relative to a traditional non-fluorinated fullerene by fluorinating the donor molecule as well.« less

Comparison of small molecules and oligonucleotides that target a toxic, non-coding RNA.

PubMed

Costales, Matthew G; Rzuczek, Suzanne G; Disney, Matthew D

2016-06-01

Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)(exp)) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example. Copyright © 2016. Published by Elsevier Ltd.

In Situ Oxidation Synthesis of p-Type Composite with Narrow-Bandgap Small Organic Molecule Coating on Single-Walled Carbon Nanotube: Flexible Film and Thermoelectric Performance.

PubMed

Gao, Caiyan; Chen, Guangming

2018-03-01

Although composites of organic polymers or n-type small molecule/carbon nanotube (CNT) have achieved significant advances in thermoelectric (TE) applications, p-type TE composites of small organic molecules as thick surface coating layers on the surfaces of inorganic nanoparticles still remain a great challenge. Taking advantage of in situ oxidation reaction of thieno[3,4-b]pyrazine (TP) into TP di-N-oxide (TPNO) on single-walled CNT (SWCNT) surface, a novel synthesis strategy is proposed to achieve flexible films of TE composites with narrow-bandgap (1.19 eV) small molecule coating on SWCNT surface. The TE performance can be effectively enhanced and conveniently tuned by poly(sodium-p-styrenesulfonate) content, TPNO/SWCNT mass ratio, and posttreatment by various polar solvents. The maximum of the composite power factor at room temperature is 29.4 ± 1.0 µW m -1 K -2 . The work presents a way to achieve flexible films of p-type small organic molecule/inorganic composites with clear surface coating morphology for TE application. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measurement of Small Molecular Dopant F4TCNQ and C 60F 36 Diffusion in Organic Bilayer Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun; Rochester, Chris W.; Jacobs, Ian E.

2015-12-03

The diffusion of molecules through and between organic layers is a serious stability concern in organic electronic devices. In this paper, the temperature-dependent diffusion of molecular dopants through small molecule hole transport layers is observed. Specifically we investigate bilayer stacks of small molecules used for hole transport (MeO-TPD) and p-type dopants (F4TCNQ and C 60F 36) used in hole injection layers for organic light emitting diodes and hole collection electrodes for organic photovoltaics. With the use of absorbance spectroscopy, photoluminescence spectroscopy, neutron reflectometry, and near-edge X-ray absorption fine structure spectroscopy, we are able to obtain a comprehensive picture of themore » diffusion of fluorinated small molecules through MeO-TPD layers. F4TCNQ spontaneously diffuses into the MeO-TPD material even at room temperature, while C 60F 36, a much bulkier molecule, is shown to have a substantially higher morphological stability. Finally, this study highlights that the differences in size/geometry and thermal properties of small molecular dopants can have a significant impact on their diffusion in organic device architectures.« less

A semantic web ontology for small molecules and their biological targets.

PubMed

Choi, Jooyoung; Davis, Melissa J; Newman, Andrew F; Ragan, Mark A

2010-05-24

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and UniProt, and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery.

Small molecules as therapy for uveitis: a selected perspective of new and developing agents.

PubMed

Pleyer, Uwe; Algharably, Engi Abdel-Hady; Feist, Eugen; Kreutz, Reinhold

2017-09-01

Intraocular inflammation (uveitis) remains a significant burden of legal blindness. Because of its immune mediated and chronic recurrent nature, common therapy includes corticosteroids, disease-modifying anti-rheumatic drugs and more recently biologics as immune modulatory agents. The purpose of this article is to identify the role of new treatment approaches focusing on small molecules as therapeutic option in uveitis. Areas covered: A MEDLINE database search was conducted through February 2017 using the terms 'uveitis' and 'small molecule'. To provide ongoing and future perspectives in treatment options, also clinical trials as registered at ClinicalTrials.gov were included. Both, results from experimental as well as clinical research in this field were included. Since this field is rapidly evolving, a selection of promising agents had to be made. Expert opinion: Small molecules may interfere at different steps of the inflammatory cascade and appear as an interesting option in the treatment algorithm of uveitis. Because of their highly targeted molecular effects and their favorable bioavailability with the potential of topical application small molecules hold great promise. Nevertheless, a careful evaluation of these agents has to be made, since current experience is almost exclusively based on experimental uveitis models and few registered trials.

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS.

PubMed

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-04-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H] - ) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. Graphical Abstract ᅟ.

Exporters for Production of Amino Acids and Other Small Molecules.

PubMed

Eggeling, Lothar

Microbes are talented catalysts to synthesize valuable small molecules in their cytosol. However, to make full use of their skills - and that of metabolic engineers - the export of intracellularly synthesized molecules to the culture medium has to be considered. This step is as essential as is each step for the synthesis of the favorite molecule of the metabolic engineer, but is frequently not taken into account. To export small molecules via the microbial cell envelope, a range of different types of carrier proteins is recognized to be involved, which are primary active carriers, secondary active carriers, or proteins increasing diffusion. Relevant export may require just one carrier as is the case with L-lysine export by Corynebacterium glutamicum or involve up to four carriers as known for L-cysteine excretion by Escherichia coli. Meanwhile carriers for a number of small molecules of biotechnological interest are recognized, like for production of peptides, nucleosides, diamines, organic acids, or biofuels. In addition to carriers involved in amino acid excretion, such carriers and their impact on product formation are described, as well as the relatedness of export carriers which may serve as a hint to identify further carriers required to improve product formation by engineering export.

Canopy gaps and dead tree dynamics: poking holes in the forest.

Treesearch

Sally Duncan

2002-01-01

When large trees die, individually or in clumps, gaps are opened in the forest canopy. A shifting mosaic of patches, from small single-tree gaps to very large gaps caused by wildlife, is a natural part of the development of composition and structure in mature forests. Gaps increase the diversity of forests across the landscape and present local environments that...

Reaction-based small-molecule fluorescent probes for dynamic detection of ROS and transient redox changes in living cells and small animals.

PubMed

Lü, Rui

2017-09-01

Dynamic detection of transient redox changes in living cells and animals has broad implications for human health and disease diagnosis, because intracellular redox homeostasis regulated by reactive oxygen species (ROS) plays important role in cell functions, normal physiological functions and some serious human diseases (e.g., cancer, Alzheimer's disease, diabetes, etc.) usually have close relationship with the intracellular redox status. Small-molecule ROS-responsive fluorescent probes can act as powerful tools for dynamic detection of ROS and redox changes in living cells and animals through fluorescence imaging techniques; and great advances have been achieved recently in the design and synthesis of small-molecule ROS-responsive fluorescent probes. This article highlights up-to-date achievements in designing and using the reaction-based small-molecule fluorescent probes (with high sensitivity and selectivity to ROS and redox cycles) in the dynamic detection of ROS and transient redox changes in living cells and animals through fluorescence imaging. Copyright © 2017. Published by Elsevier Ltd.

The Endoplasmic Reticulum Membrane Is Permeable to Small Molecules

PubMed Central

Le Gall, Sylvie; Neuhof, Andrea; Rapoport, Tom

2004-01-01

The lumen of the endoplasmic reticulum (ER) differs from the cytosol in its content of ions and other small molecules, but it is unclear whether the ER membrane is as impermeable as other membranes in the cell. Here, we have tested the permeability of the ER membrane to small, nonphysiological molecules. We report that isolated ER vesicles allow different chemical modification reagents to pass from the outside into the lumen with little hindrance. In permeabilized cells, the ER membrane allows the passage of a small, charged modification reagent that is unable to cross the plasma membrane or the lysosomal and trans-Golgi membranes. A larger polar reagent of ∼5 kDa is unable to pass through the ER membrane. Permeation of the small molecules is passive because it occurs at low temperature in the absence of energy. These data indicate that the ER membrane is significantly more leaky than other cellular membranes, a property that may be required for protein folding and other functions of the ER. PMID:14617815

First-principles investigation on defect-induced silicene nanoribbons - A superior media for sensing NH3, NO2 and NO gas molecules

NASA Astrophysics Data System (ADS)

Walia, Gurleen Kaur; Randhawa, Deep Kamal Kaur

2018-04-01

In this paper, the electronic and transport properties of armchair silicene nanoribbons (ASiNRs) are analyzed for their application as highly selective and sensitive gas molecule sensors. The study is focused on sensing three nitrogen based gases; ammonia (NH3), nitrogen dioxide (NO2) and nitric oxide (NO), which depending upon their adsorption energy and charge transfer, form bonds of varying strength with ASiNRs. The negligible band gap of ASiNRs is tuned by adding a defect in ASiNRs. Adsorption of NH3 leads to the opening of band gap whereas on adsorption of NO2 and NO, ASiNRs exhibit metallic nature. Distinctly divergent electronic and transport properties of ASiNRs are observed and on adsorption of NH3, NO2 and NO, renders them suitable for sensing them. All gas molecules show stronger adsorption on defective ASiNRs (D-ASiNRs) as compared to pristine ASiNRs (P-ASiNRs). The work reveals that introduction of defect can drastically improve the sensitivity of ASiNRs.

Cucurbituril mediated single molecule detection and identification via recognition tunneling.

PubMed

Xiao, Bohuai; Liang, Feng; Liu, Simin; Im, JongOne; Li, Yunchuan; Liu, Jing; Zhang, Bintian; Zhou, Jianghao; He, Jin; Chang, Shuai

2018-06-08

Recognition tunneling (RT) is an emerging technique for investigating single molecules in a tunnel junction. We have previously demonstrated its capability of single molecule detection and identification, as well as probing the dynamics of intermolecular bonding at the single molecule level. Here by introducing cucurbituril as a new class of recognition molecule, we demonstrate a powerful platform for electronically investigating the host-guest chemistry at single molecule level. In this report, we first investigated the single molecule electrical properties of cucurbituril in a tunnel junction. Then we studied two model guest molecules, aminoferrocene and amantadine, which were encapsulated by cucurbituril. Small differences in conductance and lifetime can be recognized between the host-guest complexes with the inclusion of different guest molecules. By using a machine learning algorithm to classify the RT signals in a hyper dimensional space, the accuracy of guest molecule recognition can be significantly improved, suggesting the possibility of using cucurbituril molecule for single molecule identification. This work enables a new class of recognition molecule for RT technique and opens the door for detecting a vast variety of small molecules by electrical measurements.

Plasmonic tunnel junctions for single-molecule redox chemistry.

PubMed

de Nijs, Bart; Benz, Felix; Barrow, Steven J; Sigle, Daniel O; Chikkaraddy, Rohit; Palma, Aniello; Carnegie, Cloudy; Kamp, Marlous; Sundararaman, Ravishankar; Narang, Prineha; Scherman, Oren A; Baumberg, Jeremy J

2017-10-20

Nanoparticles attached just above a flat metallic surface can trap optical fields in the nanoscale gap. This enables local spectroscopy of a few molecules within each coupled plasmonic hotspot, with near thousand-fold enhancement of the incident fields. As a result of non-radiative relaxation pathways, the plasmons in such sub-nanometre cavities generate hot charge carriers, which can catalyse chemical reactions or induce redox processes in molecules located within the plasmonic hotspots. Here, surface-enhanced Raman spectroscopy allows us to track these hot-electron-induced chemical reduction processes in a series of different aromatic molecules. We demonstrate that by increasing the tunnelling barrier height and the dephasing strength, a transition from coherent to hopping electron transport occurs, enabling observation of redox processes in real time at the single-molecule level.

An application of small-gap equations in sealing devices

NASA Technical Reports Server (NTRS)

Vionnet, Carlos A.; Heinrich, Juan C.

1993-01-01

The study of a thin, incompressible Newtonian fluid layer trapped between two almost parallel, sliding surfaces has been actively pursued in the last decades. This subject includes lubrication applications such as slider bearings or the sealing of non-pressurized fluids with rubber rotary shaft seals. In the present work we analyze numerically the flow of lubricant fluid through a micro-gap of sealing devices. The first stage of this study is carried out assuming that a 'small-gap' parameter delta attains an extreme value in the Navier-Stokes equations. The precise meaning of small-gap is achieved by the particular limit delta = 0 which, within the bounds of the hypotheses, predicts transport of lubricant through the sealed area by centrifugal instabilities. Numerical results obtained with the penalty function approximation in the finite element method are presented. In particular, the influence of inflow and outflow boundary conditions, and their impact in the simulated flow, are discussed.

An application of small-gap equations in sealing devices

NASA Astrophysics Data System (ADS)

Vionnet, Carlos A.; Heinrich, Juan C.

1993-11-01

The study of a thin, incompressible Newtonian fluid layer trapped between two almost parallel, sliding surfaces has been actively pursued in the last decades. This subject includes lubrication applications such as slider bearings or the sealing of non-pressurized fluids with rubber rotary shaft seals. In the present work we analyze numerically the flow of lubricant fluid through a micro-gap of sealing devices. The first stage of this study is carried out assuming that a 'small-gap' parameter delta attains an extreme value in the Navier-Stokes equations. The precise meaning of small-gap is achieved by the particular limit delta = 0 which, within the bounds of the hypotheses, predicts transport of lubricant through the sealed area by centrifugal instabilities. Numerical results obtained with the penalty function approximation in the finite element method are presented. In particular, the influence of inflow and outflow boundary conditions, and their impact in the simulated flow, are discussed.

Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification.

PubMed

Yao, Yongpeng; Li, Shanshan; Cao, Jiaqian; Liu, Weiwei; Fan, Keqiang; Xiang, Wensheng; Yang, Keqian; Kong, Deming; Wang, Weishan

2018-05-08

Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.

A structural biology perspective on bioactive small molecules and their plant targets.

PubMed

Kumari, Selva; van der Hoorn, Renier A L

2011-10-01

Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design. Copyright © 2011 Elsevier Ltd. All rights reserved.

New developments in microbial interspecies signaling.

PubMed

Shank, Elizabeth Anne; Kolter, Roberto

2009-04-01

There is a growing appreciation that in addition to well-documented intraspecies quorum sensing systems, small molecules act as signals between microbes of different species. This review will focus on how bacterial small molecules modulate these interspecies interactions. We will particularly emphasize complex relationships such as those between microbes and insects, interactions resulting in non-antagonistic outcomes (i.e. developmental and morphological processes), how co-culture can lead to the discovery of new small molecules, and the use of known compounds to evoke unexpected responses and mediate crosstalk between microbes.

Tailoring the interface using thiophene small molecules in TiO2/P3HT hybrid solar cells.

PubMed

Freitas, Flavio S; Clifford, John N; Palomares, Emilio; Nogueira, Ana F

2012-09-14

In this paper we focus on the effect of carboxylated thiophene small molecules as interface modifiers in TiO(2)/P3HT hybrid solar cells. Our results show that small differences in the chemical structure of these molecules, for example, the presence of the -CH(2)- group in the 2-thiopheneacetic acid (TAA), can greatly increase the TiO(2) surface wettability, improving the TiO(2)/polymer contact. This effect is important to enhance exciton splitting and charge separation.

Janus Kinase Antagonists and Other Novel Small Molecules for the Treatment of Crohn's Disease.

PubMed

Boland, Brigid S; Vermeire, Séverine

2017-09-01

There is an ongoing, unmet need for effective therapies for Crohn's disease. Treatments for Crohn's disease continue to evolve from the traditional biologics to novel small molecules, with targeted mechanisms directed toward pathways that are dysregulated in Crohn's disease. There are multiple emerging mechanisms of action, including Janus kinase inhibition, Smad7 inhibition, and sphingosine-1-phosphate receptor modulators, that are administered as oral medications, and small molecules represent the next generation of therapies for Crohn's disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Gap characteristics of southeastern Ohio second-growth forests

Treesearch

David M. Hix; Katherine K. Helfrich

2003-01-01

Transect sampling was used to assess the features of 30 gaps encountered in upland oak stands on the Wayne National Forest. Tip-ups caused the most canopy gaps (52 percent), two-thirds of which were small (

Theoretical Investigation of Single-Molecule Sensing Using Nanotube-Enhanced Circular Dichroism.

PubMed

Silva, Jaime; Milne, Bruce F; Nogueira, Fernando

2018-06-19

First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single-molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate their CD response. Large induced CD (ICD) effects, differing for each test molecule, were observed in all SWCNT-molecule complexes. As the SWCNT used in this study shows no intrinsic CD response, the ICD spectra are the result of interaction with the small molecules. This finding is general and independent of the (a)chiral nature of the adsorbed molecule. Our results indicate that it is possible to design a system that uses SWCNT for detection of molecules using the change in CD spectrum of the system induced by adsorption of the molecule onto the SWCNT surface.

2016 White Paper on recent issues in bioanalysis: focus on biomarker assay validation (BAV) (Part 1 - small molecules, peptides and small molecule biomarkers by LCMS).

PubMed

Yang, Eric; Welink, Jan; Cape, Stephanie; Woolf, Eric; Sydor, Jens; James, Christopher; Goykhman, Dina; Arnold, Mark; Addock, Neil; Bauer, Ronald; Buonarati, Michael; Ciccimaro, Eugene; Dodda, Raj; Evans, Christopher; Garofolo, Fabio; Hughes, Nicola; Islam, Rafiq; Nehls, Corey; Wilson, Amanda; Briscoe, Chad; Bustard, Mark; Coppola, Laura; Croft, Stephanie; Drexler, Dieter; Ferrari, Luca; Fraier, Daniela; Jenkins, Rand; Kadavil, John; King, Lloyd; Li, Wenkui; Lima Santos, Gustavo Mendes; Musuku, Adrien; Ramanathan, Ragu; Saito, Yoshiro; Savoie, Natasha; Summerfield, Scott; Sun, Rachel; Tampal, Nilufer; Vinter, Steve; Wakelin-Smith, Jason; Yue, Qin

2016-10-07

The 2016 10 th Workshop on Recent Issues in Bioanalysis (10 th WRIB) took place in Orlando, Florida with participation of close to 700 professionals from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. WRIB was once again a 5-day, weeklong event - A Full Immersion Week of Bioanalysis including Biomarkers and Immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small and large molecule analysis involving LCMS, hybrid LBA/LCMS, and LBA approaches, with the focus on biomarkers and immunogenicity. This 2016 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. This white paper is published in 3 parts due to length. This part (Part 1) discusses the recommendations for small molecules, peptides and small molecule biomarkers by LCMS. Part 2 (Hybrid LBA/LCMS and regulatory inputs from major global health authorities) and Part 3 (large molecule bioanalysis using LBA, biomarkers and immunogenicity) will be published in the Bioanalysis journal, issue 23.

Diffusion of small molecules into medaka embryos improved by electroporation

PubMed Central

2013-01-01

Background Diffusion of small molecules into fish embryos is essential for many experimental procedures in developmental biology and toxicology. Since we observed a weak uptake of lithium into medaka eggs we started a detailed analysis of its diffusion properties using small fluorescent molecules. Results Contrary to our expectations, not the rigid outer chorion but instead membrane systems surrounding the embryo/yolk turned out to be the limiting factor for diffusion into medaka eggs. The consequence is a bi-phasic uptake of small molecules first reaching the pervitelline space with a diffusion half-time in the range of a few minutes. This is followed by a slow second phase (half-time in the range of several hours) during which accumulation in the embryo/yolk takes place. Treatment with detergents improved the uptake, but strongly affected the internal distribution of the molecules. Testing electroporation we could establish conditions to overcome the diffusion barrier. Applying this method to lithium chloride we observed anterior truncations in medaka embryos in agreement with its proposed activation of Wnt signalling. Conclusions The diffusion of small molecules into medaka embryos is slow, caused by membrane systems underneath the chorion. These results have important implications for pharmacologic/toxicologic techniques like the fish embryo test, which therefore require extended incubation times in order to reach sufficient concentrations in the embryos. PMID:23815821

Homeostasis in the vertebrate lens: mechanisms of solute exchange

PubMed Central

Dahm, Ralf; van Marle, Jan; Quinlan, Roy A.; Prescott, Alan R.; Vrensen, Gijs F. J. M.

2011-01-01

The eye lens is avascular, deriving nutrients from the aqueous and vitreous humours. It is, however, unclear which mechanisms mediate the transfer of solutes between these humours and the lens' fibre cells (FCs). In this review, we integrate the published data with the previously unpublished ultrastructural, dye loading and magnetic resonance imaging results. The picture emerging is that solute transfer between the humours and the fibre mass is determined by four processes: (i) paracellular transport of ions, water and small molecules along the intercellular spaces between epithelial and FCs, driven by Na+-leak conductance; (ii) membrane transport of such solutes from the intercellular spaces into the fibre cytoplasm by specific carriers and transporters; (iii) gap-junctional coupling mediating solute flux between superficial and deeper fibres, Na+/K+-ATPase-driven efflux of waste products in the equator, and electrical coupling of fibres; and (iv) transcellular transfer via caveoli and coated vesicles for the uptake of macromolecules and cholesterol. There is evidence that the Na+-driven influx of solutes occurs via paracellular and membrane transport and the Na+/K+-ATPase-driven efflux of waste products via gap junctions. This micro-circulation is likely restricted to the superficial cortex and nearly absent beyond the zone of organelle loss, forming a solute exchange barrier in the lens. PMID:21402585

Experimental simulation of radiation damage of polymers in space applications by cosmic-ray-type high energy heavy ions and the resulting changes in optical properties

NASA Astrophysics Data System (ADS)

Hossain, U. H.; Ensinger, W.

2015-12-01

Devices operating in space, e.g. in satellites, are being hit by cosmic rays. These include so-called HZE-ions, with High mass (Z) and energy (E). These highly energetic heavy ions penetrate deeply into the materials and deposit a large amount of energy, typically several keV per nm range. Serious damage is created. In space vehicles, polymers are used which are degraded under ion bombardment. HZE ion irradiation can experimentally be simulated in large scale accelerators. In the present study, the radiation damage of aliphatic vinyl- and fluoro-polymers by heavy ions with energies in the GeV range is described. The ions cause bond scission and create volatile small molecular species, leading to considerable mass loss of the polymers. Since hydrogen, oxygen and fluorine-containing molecules are created and these elements are depleted, the remaining material is carbon-richer than the original polymers and contains conjugated CC double bonds. This process is investigated by measuring the optical band gap with UV-Vis absorption spectrometry as a function of ion fluence. The results show how the optical band gaps shift from the UV into the Vis region upon ion irradiation for the different polymers.

Test systems in drug discovery for hazard identification and risk assessment of human drug-induced liver injury.

PubMed

Weaver, Richard J; Betts, Catherine; Blomme, Eric A G; Gerets, Helga H J; Gjervig Jensen, Klaus; Hewitt, Philip G; Juhila, Satu; Labbe, Gilles; Liguori, Michael J; Mesens, Natalie; Ogese, Monday O; Persson, Mikael; Snoeys, Jan; Stevens, James L; Walker, Tracy; Park, B Kevin

2017-07-01

The liver is an important target for drug-induced toxicities. Early detection of hepatotoxic drugs requires use of well-characterized test systems, yet current knowledge, gaps and limitations of tests employed remains an important issue for drug development. Areas Covered: The current state of the science, understanding and application of test systems in use for the detection of drug-induced cytotoxicity, mitochondrial toxicity, cholestasis and inflammation is summarized. The test systems highlighted herein cover mostly in vitro and some in vivo models and endpoint measurements used in the assessment of small molecule toxic liabilities. Opportunities for research efforts in areas necessitating the development of specific tests and improved mechanistic understanding are highlighted. Expert Opinion: Use of in vitro test systems for safety optimization will remain a core activity in drug discovery. Substantial inroads have been made with a number of assays established for human Drug-induced Liver Injury. There nevertheless remain significant gaps with a need for improved in vitro tools and novel tests to address specific mechanisms of human Drug-Induced Liver Injury. Progress in these areas will necessitate not only models fit for application, but also mechanistic understanding of how chemical insult on the liver occurs in order to identify translational and quantifiable readouts for decision-making.

Connexin-Mediated Functional and Metabolic Coupling Between Astrocytes and Neurons.

PubMed

Mayorquin, Lady C; Rodriguez, Andrea V; Sutachan, Jhon-Jairo; Albarracín, Sonia L

2018-01-01

The central nervous system (CNS) requires sophisticated regulation of neuronal activity. This modulation is partly accomplished by non-neuronal cells, characterized by the presence of transmembrane gap junctions (GJs) and hemichannels (HCs). This allows small molecule diffusion to guarantee neuronal synaptic activity and plasticity. Astrocytes are metabolically and functionally coupled to neurons by the uptake, binding and recycling of neurotransmitters. In addition, astrocytes release metabolites, such as glutamate, glutamine, D-serine, adenosine triphosphate (ATP) and lactate, regulating synaptic activity and plasticity by pre- and postsynaptic mechanisms. Uncoupling neuroglial communication leads to alterations in synaptic transmission that can be detrimental to neuronal circuit function and behavior. Therefore, understanding the pathways and mechanisms involved in this intercellular communication is fundamental for the search of new targets that can be used for several neurological disease treatments. This review will focus on molecular mechanisms mediating physiological and pathological coupling between astrocytes and neurons through GJs and HCs.

Protein recognition by a pattern-generating fluorescent molecular probe.

PubMed

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

SERS of Individual Nanoparticles on a Mirror: Size Does Matter, but so Does Shape

PubMed Central

2016-01-01

Coupling noble metal nanoparticles by a 1 nm gap to an underlying gold mirror confines light to extremely small volumes, useful for sensing on the nanoscale. Individually measuring 10 000 of such gold nanoparticles of increasing size dramatically shows the different scaling of their optical scattering (far-field) and surface-enhanced Raman emission (SERS, near-field). Linear red-shifts of the coupled plasmon modes are seen with increasing size, matching theory. The total SERS from the few hundred molecules under each nanoparticle dramatically increases with increasing size. This scaling shows that maximum SERS emission is always produced from the largest nanoparticles, irrespective of tuning to any plasmonic resonances. Changes of particle facet with nanoparticle size result in vastly weaker scaling of the near-field SERS, without much modifying the far-field, and allows simple approaches for optimizing practical sensing. PMID:27223478

SERS of Individual Nanoparticles on a Mirror: Size Does Matter, but so Does Shape.

PubMed

Benz, Felix; Chikkaraddy, Rohit; Salmon, Andrew; Ohadi, Hamid; de Nijs, Bart; Mertens, Jan; Carnegie, Cloudy; Bowman, Richard W; Baumberg, Jeremy J

2016-06-16

Coupling noble metal nanoparticles by a 1 nm gap to an underlying gold mirror confines light to extremely small volumes, useful for sensing on the nanoscale. Individually measuring 10 000 of such gold nanoparticles of increasing size dramatically shows the different scaling of their optical scattering (far-field) and surface-enhanced Raman emission (SERS, near-field). Linear red-shifts of the coupled plasmon modes are seen with increasing size, matching theory. The total SERS from the few hundred molecules under each nanoparticle dramatically increases with increasing size. This scaling shows that maximum SERS emission is always produced from the largest nanoparticles, irrespective of tuning to any plasmonic resonances. Changes of particle facet with nanoparticle size result in vastly weaker scaling of the near-field SERS, without much modifying the far-field, and allows simple approaches for optimizing practical sensing.

Advanced protein formulations

PubMed Central

Wang, Wei

2015-01-01

It is well recognized that protein product development is far more challenging than that for small-molecule drugs. The major challenges include inherent sensitivity to different types of stresses during the drug product manufacturing process, high rate of physical and chemical degradation during long-term storage, and enhanced aggregation and/or viscosity at high protein concentrations. In the past decade, many novel formulation concepts and technologies have been or are being developed to address these product development challenges for proteins. These concepts and technologies include use of uncommon/combination of formulation stabilizers, conjugation or fusion with potential stabilizers, site-specific mutagenesis, and preparation of nontraditional types of dosage forms—semiaqueous solutions, nonfreeze-dried solid formulations, suspensions, and other emerging concepts. No one technology appears to be mature, ideal, and/or adequate to address all the challenges. These gaps will likely remain in the foreseeable future and need significant efforts for ultimate resolution. PMID:25858529

Protein recognition by a pattern-generating fluorescent molecular probe

NASA Astrophysics Data System (ADS)

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Luning; Neuscamman, Eric

We present a modification to variational Monte Carlo’s linear method optimization scheme that addresses a critical memory bottleneck while maintaining compatibility with both the traditional ground state variational principle and our recently-introduced variational principle for excited states. For wave function ansatzes with tens of thousands of variables, our modification reduces the required memory per parallel process from tens of gigabytes to hundreds of megabytes, making the methodology a much better fit for modern supercomputer architectures in which data communication and per-process memory consumption are primary concerns. We verify the efficacy of the new optimization scheme in small molecule tests involvingmore » both the Hilbert space Jastrow antisymmetric geminal power ansatz and real space multi-Slater Jastrow expansions. Satisfied with its performance, we have added the optimizer to the QMCPACK software package, with which we demonstrate on a hydrogen ring a prototype approach for making systematically convergent, non-perturbative predictions of Mott-insulators’ optical band gaps.« less

Effect of co-crystallization on singlet fission efficiency in pentacene derivatives

NASA Astrophysics Data System (ADS)

Wang, Xiaopeng; Sanders, Samuel; Campos, Luis; Sfeir, Matthew; Marom, Noa

Singlet fission (SF), the conversion of one singlet exciton into two triplet excitons, may lead to a twofold increase in the efficiency of organic photovoltaics. Since SF has been observed in crystalline pentacene, this material has drawn interest both experimentally and theoretically. Recently, it has been shown that SF efficiency in rubrene may be improved by modifying the crystal packing. Here, we study the effect of co-crystallization with small molecule H-bond donors on SF efficiency in pentacene derivatives. Five co-crystals are synthetized and their photoluminescence (PL) and absorption spectra are measured. First-principles calculations based on many-body perturbation theory (MBPT) are then employed to study their excitonic properties. By combining experiment and theory, we demonsrate that excitonic properties, including singlet-triplet gaps, exciton binding energies, and exciton localization, are significantly modulated in pentacene co-crystals. Consequently, co-crystallization becomes an effective strategy for improving SF efficiency in molecular crystals of organic semiconductors.

Structural, vibrational and nuclear magnetic resonance investigations of 4-bromoisoquinoline by experimental and theoretical DFT methods.

PubMed

Arjunan, V; Thillai Govindaraja, S; Jayapraksh, A; Mohan, S

2013-04-15

Quantum chemical calculations of energy, structural parameters and vibrational wavenumbers of 4-bromoisoquinoline (4BIQ) were carried out by using B3LYP method using 6-311++G(**), cc-pVTZ and LANL2DZ basis sets. The optimised geometrical parameters obtained by DFT calculations are in good agreement with electron diffraction data. Interpretations of the experimental FTIR and FT-Raman spectra have been reported with the aid of the theoretical wavenumbers. The differences between the observed and scaled wavenumber values of most of the fundamentals are very small. The thermodynamic parameters have also been computed. Electronic properties of the molecule were discussed through the molecular electrostatic potential surface, HOMO-LUMO energy gap and NBO analysis. To provide precise assignments of (1)H and (13)CNMR spectra, isotropic shielding and chemical shifts were calculated with the Gauge-Invariant Atomic Orbital (GIAO) method. Copyright © 2013 Elsevier B.V. All rights reserved.

How Proteins Bind Macrocycles

PubMed Central

Villar, Elizabeth A.; Beglov, Dmitri; Chennamadhavuni, Spandan; Porco, John A.; Kozakov, Dima; Vajda, Sandor; Whitty, Adrian

2014-01-01

The potential utility of synthetic macrocycles as drugs, particularly against low druggability targets such as protein-protein interactions, has been widely discussed. There is little information, however, to guide the design of macrocycles for good target protein-binding activity or bioavailability. To address this knowledge gap we analyze the binding modes of a representative set of macrocycle-protein complexes. The results, combined with consideration of the physicochemical properties of approved macrocyclic drugs, allow us to propose specific guidelines for the design of synthetic macrocycles libraries possessing structural and physicochemical features likely to favor strong binding to protein targets and also good bioavailability. We additionally provide evidence that large, natural product derived macrocycles can bind to targets that are not druggable by conventional, drug-like compounds, supporting the notion that natural product inspired synthetic macrocycles can expand the number of proteins that are druggable by synthetic small molecules. PMID:25038790

Random-Phase Approximation Methods

NASA Astrophysics Data System (ADS)

Chen, Guo P.; Voora, Vamsee K.; Agee, Matthew M.; Balasubramani, Sree Ganesh; Furche, Filipp

2017-05-01

Random-phase approximation (RPA) methods are rapidly emerging as cost-effective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed. The ability of RPA to approximately capture static correlation in molecules is quantified by an analysis of RPA natural occupation numbers. We illustrate the use of RPA methods in applications to small-gap systems such as open-shell d- and f-element compounds, radicals, and weakly bound complexes, where semilocal density functional results exhibit strong functional dependence.

Connexins: Intercellular Signal Transmitters in Lymphohematopoietic Tissues.

PubMed

González-Nieto, Daniel; Chang, Kyung-Hee; Fasciani, Ilaria; Nayak, Ramesh; Fernandez-García, Laura; Barrio, Luis C; Cancelas, José A

2015-01-01

Life-long hematopoietic demands are met by a pool of hematopoietic stem cells (HSC) with self-renewal and multipotential differentiation ability. Humoral and paracrine signals from the bone marrow (BM) hematopoietic microenvironment control HSC activity. Cell-to-cell communication through connexin (Cx) containing gap junctions (GJs) allows pluricellular coordination and synchronization through transfer of small molecules with messenger activity. Hematopoietic and surrounding nonhematopoietic cells communicate each other through GJs, which regulate fetal and postnatal HSC content and function in hematopoietic tissues. Traffic of HSC between peripheral blood and BM is also dependent on Cx proteins. Cx mutations are associated with human disease and hematopoietic dysfunction and Cx signaling may represent a target for therapeutic intervention. In this review, we illustrate and highlight the importance of Cxs in the regulation of hematopoietic homeostasis under normal and pathological conditions. Copyright © 2015 Elsevier Inc. All rights reserved.

Small molecules targeting LapB protein prevent Listeria attachment to catfish muscle

PubMed Central

Das, Bhaskar; Lawrence, Mark

2017-01-01

Listeria monocytogenes is a Gram-positive foodborne pathogen and the causative agent of listeriosis. L. monocytogenes lapB gene encodes a cell wall surface anchor protein, and mutation of this gene causes Listeria attenuation in mice. In this work, the potential role of Listeria LapB protein in catfish fillet attachment was investigated. To achieve this, boron-based small molecules designed to interfere with the active site of the L. monocytogenes LapB protein were developed, and their ability to prevent L. monocytogenes attachment to fish fillet was tested. Results indicated that seven out of nine different small molecules were effective in reducing the Listeria attachment to catfish fillets. Of these, three small molecules (SM3, SM5, and SM7) were highly effective in blocking Listeria attachment to catfish fillets. This study suggests an alternative strategy for reduction of L. monocytogenes contamination in fresh and frozen fish products. PMID:29253892

Incorporation of ionic liquid into porous polymer monoliths to enhance the separation of small molecules in reversed-phase high-performance liquid chromatography.

PubMed

Wang, Jiafei; Bai, Ligai; Wei, Zhen; Qin, Junxiao; Ma, Yamin; Liu, Haiyan

2015-06-01

An ionic liquid was incorporated into the porous polymer monoliths to afford stationary phases with enhanced chromatographic performance for small molecules in reversed-phase high-performance liquid chromatography. The effect of the ionic liquid in the polymerization mixture on the performance of the monoliths was studied in detail. While monoliths without ionic liquid exhibited poor resolution and low efficiency, the addition of ionic liquid to the polymerization mixture provides highly increased resolution and high efficiency. The chromatographic performances of the monoliths were demonstrated by the separations of various small molecules including aromatic hydrocarbons, isomers, and homologues using a binary polar mobile phase. The present column efficiency reached 27 000 plates/m, which showed that the ionic liquid monoliths are alternative stationary phases in the separation of small molecules by high-performance liquid chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Precise small molecule recognition of a toxic CUG RNA repeat expansion

PubMed Central

Rzuczek, Suzanne G; Colgan, Lesley A; Nakai, Yoshio; Cameron, Michael D; Furling, Denis; Yasuda, Ryohei; Disney, Matthew D

2017-01-01

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context. PMID:27941760

Precise small-molecule recognition of a toxic CUG RNA repeat expansion.

PubMed

Rzuczek, Suzanne G; Colgan, Lesley A; Nakai, Yoshio; Cameron, Michael D; Furling, Denis; Yasuda, Ryohei; Disney, Matthew D

2017-02-01

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG) exp ) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG) exp . In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG) exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG) exp in its natural context.

Small molecule alteration of RNA sequence in cells and animals.

PubMed

Guan, Lirui; Luo, Yiling; Ja, William W; Disney, Matthew D

2017-10-18

RNA regulation and maintenance are critical for proper cell function. Small molecules that specifically alter RNA sequence would be exceptionally useful as probes of RNA structure and function or as potential therapeutics. Here, we demonstrate a photochemical approach for altering the trinucleotide expanded repeat causative of myotonic muscular dystrophy type 1 (DM1), r(CUG) exp . The small molecule, 2H-4-Ru, binds to r(CUG) exp and converts guanosine residues to 8-oxo-7,8-dihydroguanosine upon photochemical irradiation. We demonstrate targeted modification upon irradiation in cell culture and in Drosophila larvae provided a diet containing 2H-4-Ru. Our results highlight a general chemical biology approach for altering RNA sequence in vivo by using small molecules and photochemistry. Furthermore, these studies show that addition of 8-oxo-G lesions into RNA 3' untranslated regions does not affect its steady state levels. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-Throughput RT-PCR for small-molecule screening assays

PubMed Central

Bittker, Joshua A.

2012-01-01

Quantitative measurement of the levels of mRNA expression using real-time reverse transcription polymerase chain reaction (RT-PCR) has long been used for analyzing expression differences in tissue or cell lines of interest. This method has been used somewhat less frequently to measure the changes in gene expression due to perturbagens such as small molecules or siRNA. The availability of new instrumentation for liquid handling and real-time PCR analysis as well as the commercial availability of start-to-finish kits for RT-PCR has enabled the use of this method for high-throughput small-molecule screening on a scale comparable to traditional high-throughput screening (HTS) assays. This protocol focuses on the special considerations necessary for using quantitative RT-PCR as a primary small-molecule screening assay, including the different methods available for mRNA isolation and analysis. PMID:23487248

Selective inhibition of c-Myc/Max dimerization and DNA binding by small molecules.

PubMed

Kiessling, Anke; Sperl, Bianca; Hollis, Angela; Eick, Dirk; Berg, Thorsten

2006-07-01

bZip and bHLHZip protein family members comprise a large fraction of eukaryotic transcription factors and need to bind DNA in order to exert most of their fundamental biological roles. Their binding to DNA requires homo- or heterodimerization via alpha-helical domains, which generally do not contain obvious binding sites for small molecules. We have identified two small molecules, dubbed Mycro1 and Mycro2, which inhibit the protein-protein interactions between the bHLHZip proteins c-Myc and Max. Mycros are the first inhibitors of c-Myc/Max dimerization, which have been demonstrated to inhibit DNA binding of c-Myc with preference over other dimeric transcription factors in vitro. Mycros inhibit c-Myc-dependent proliferation, gene transcription, and oncogenic transformation in the low micromolar concentration range. Our data support the idea that dimeric transcription factors can be druggable even in the absence of obvious small-molecule binding pockets.

Small-molecule pheromones and hormones controlling nematode development.

PubMed

Butcher, Rebecca A

2017-05-17

The existence of small-molecule signals that influence development in Caenorhabditis elegans has been known for several decades, but only in recent years have the chemical structures of several of these signals been established. The identification of these signals has enabled connections to be made between these small molecules and fundamental signaling pathways in C. elegans that influence not only development but also metabolism, fertility, and lifespan. Spurred by these important discoveries and aided by recent advances in comparative metabolomics and NMR spectroscopy, the field of nematode chemistry has the potential to expand dramatically in the coming years. This Perspective will focus on small-molecule pheromones and hormones that influence developmental events in the nematode life cycle (ascarosides, dafachronic acids, and nemamides), will cover more recent work regarding the biosynthesis of these signals, and will explore how the discovery of these signals is transforming our understanding of nematode development and physiology.

A small molecule chemical chaperone optimizes its unfolded state contraction and denaturant like properties

NASA Astrophysics Data System (ADS)

Sharma, Sunny; Sarkar, Suparna; Paul, Simanta Sarani; Roy, Syamal; Chattopadhyay, Krishnananda

2013-12-01

Protein aggregation is believed to occur through the formation of misfolded conformations. It is expected that, in order to minimize aggregation, an effective small molecule chaperone would destabilize these intermediates. To study the mechanism of a chemical chaperone, we have designed a series of mutant proteins in which a tryptophan residue experiences different local environments and solvent exposures. We show that these mutants correspond to a series of conformationally altered proteins with varying degree of misfolding stress and aggregation propensities. Using arginine as a model small molecule, we show that a combination of unfolded state contraction and denaturant like properties results in selective targeting and destabilization of the partially folded proteins. In comparison, the effect of arginine towards the folded like control mutant, which is not aggregation prone, is significantly less. Other small molecules, lacking either of the above two properties, do not offer any specificity towards the misfolded proteins.

Side-chain Engineering of Benzo[1,2-b:4,5-b’]dithiophene Core-structured Small Molecules for High-Performance Organic Solar Cells

PubMed Central

Yin, Xinxing; An, Qiaoshi; Yu, Jiangsheng; Guo, Fengning; Geng, Yongliang; Bian, Linyi; Xu, Zhongsheng; Zhou, Baojing; Xie, Linghai; Zhang, Fujun; Tang, Weihua

2016-01-01

Three novel small molecules have been developed by side-chain engineering on benzo[1,2-b:4,5-b’]dithiophene (BDT) core. The typical acceptor-donor-acceptor (A-D-A) structure is adopted with 4,8-functionalized BDT moieties as core, dioctylterthiophene as π bridge and 3-ethylrhodanine as electron-withdrawing end group. Side-chain engineering on BDT core exhibits small but measurable effect on the optoelectronic properties of small molecules. Theoretical simulation and X-ray diffraction study reveal the subtle tuning of interchain distance between conjugated backbones has large effect on the charge transport and thus the photovoltaic performance of these molecules. Bulk-heterojunction solar cells fabricated with a configuration of ITO/PEDOT:PSS/SM:PC71BM/PFN/Al exhibit a highest power conversion efficiency (PCE) of 6.99% after solvent vapor annealing. PMID:27140224

Side-chain Engineering of Benzo[1,2-b:4,5-b']dithiophene Core-structured Small Molecules for High-Performance Organic Solar Cells.

PubMed

Yin, Xinxing; An, Qiaoshi; Yu, Jiangsheng; Guo, Fengning; Geng, Yongliang; Bian, Linyi; Xu, Zhongsheng; Zhou, Baojing; Xie, Linghai; Zhang, Fujun; Tang, Weihua

2016-05-03

Three novel small molecules have been developed by side-chain engineering on benzo[1,2-b:4,5-b']dithiophene (BDT) core. The typical acceptor-donor-acceptor (A-D-A) structure is adopted with 4,8-functionalized BDT moieties as core, dioctylterthiophene as π bridge and 3-ethylrhodanine as electron-withdrawing end group. Side-chain engineering on BDT core exhibits small but measurable effect on the optoelectronic properties of small molecules. Theoretical simulation and X-ray diffraction study reveal the subtle tuning of interchain distance between conjugated backbones has large effect on the charge transport and thus the photovoltaic performance of these molecules. Bulk-heterojunction solar cells fabricated with a configuration of ITO/PEDOT:PSS/SM:PC71BM/PFN/Al exhibit a highest power conversion efficiency (PCE) of 6.99% after solvent vapor annealing.

Small molecule solution-processed bulk heterojunction solar cells with inverted structure using porphyrin donor

NASA Astrophysics Data System (ADS)

Yamamoto, Takaki; Hatano, Junichi; Nakagawa, Takafumi; Yamaguchi, Shigeru; Matsuo, Yutaka

2013-01-01

Utilizing tetraethynyl porphyrin derivative (TE-Por) as a small molecule donor material, we fabricated a small molecule solution-processed bulk heterojunction (BHJ) solar cell with inverted structure, which exhibited 1.6% power conversion efficiency (JSC (short-circuit current) = 4.6 mA/cm2, VOC (open-circuit voltage) = 0.90 V, and FF (fill factor) = 0.39) in the device configuration indium tin oxide/TiOx (titanium sub-oxide)/[6,6]-phenyl-C61-butyric acid methyl ester:TE-Por (5:1)/MoOx (molybdenum sub-oxide)/Au under AM1.5 G illumination at 100 mW/cm2. Without encapsulation, the small molecule solution-processed inverted BHJ solar cell also showed remarkable durability to air, where it kept over 73% of its initial power conversion efficiency after storage for 28 days under ambient atmosphere in the dark.

Multivalent small molecule pan-RAS inhibitors

PubMed Central

Welsch, Matthew E.; Kaplan, Anna; Chambers, Jennifer M.; Stokes, Michael E.; Bos, Pieter H.; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A.; Huang, Christine S.; Tran, Timothy H.; Akkiraju, Hemanth; Brown, Lewis M.; Nandakumar, Renu; Cremers, Serge; Yang, Wan S.; Tong, Liang; Olive, Kenneth P.; Ferrando, Adolfo; Stockwell, Brent R.

2017-01-01

SUMMARY Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, have potential use as chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy and isothermal titration calorimetry, and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers, and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins. PMID:28235199

An open access microfluidic device for the study of the physical limits of cancer cell deformation during migration in confined environments.

PubMed

Malboubi, Majid; Jayo, Asier; Parsons, Maddy; Charras, Guillaume

2015-08-16

During metastasis, cancerous cells leave the primary tumour, pass into the circulatory system, and invade into new tissues. To migrate through the wide variety of environments they encounter, the cells must be able to remodel their cell shape efficiently to squeeze through small gaps in the extracellular matrix or extravasate into the blood stream or lymphatic system. Several studies have shown that the nucleus is the main limiting factor to migration through small gaps (Wolf et al., 2013; Harada et al., 2014; Mak et al., 2013). To understand the physical limits of cancer cell translocation in confined environments, we have fabricated a microfluidic device to study their ability to adapt their nuclear and cellular shape when passing through small gaps. The device is open access for ease of use and enables examination of the effect of different levels of spatial confinement on cell behaviour and morphology simultaneously. The results show that increasing cell confinement decreases the ability of cells to translocate into small gaps and that cells cannot penetrate into the microchannels below a threshold cross-section.

Assessment of strontium oxide functionalized graphene nanoflakes for enhanced photocatalytic activity: A density functional theory approach

NASA Astrophysics Data System (ADS)

Divya, A.; Mathavan, T.; Asath, R. Mohamed; Archana, J.; Hayakawa, Y.; Benial, A. Milton Franklin

2016-05-01

A series of strontium oxide functionalized graphene nanoflakes were designed and their optoelectronic properties were studied for enhanced photocatalytic activity. The efficiency of designed molecules was studied using various parameters such as HOMO-LUMO energy gap, light harvesting efficiency and exciton binding energy. The computed results show that by increasing the degree of functionalization of strontium oxide leads to lowering the band gap of hydrogen terminated graphene nanoflakes. Furthermore, the study explores the role of strontium oxide functionalization in Frontier Molecular Orbitals, ionization potential, electron affinity, exciton binding energy and light harvesting efficiency of designed molecules. The infrared and Raman spectra were simulated for pure and SrO functionalized graphene nanoflakes. The electron rich and electron deficient regions which are favorable for electrophilic and nucleophilic attacks respectively were analyzed using molecular electrostatic potential surface analysis.

Theoretical study of the design dye-sensitivity for usage in the solar cell device

NASA Astrophysics Data System (ADS)

Alrikabi, Alaa

There are many applications in the polymer chemistry, pharmaceutical, agricultural and industrial fields of the thiadiazole molecule and their derivatives. Allowance of the energy gap of the polymer conjugated is an object of great interesting debit for the possible removal of a doping in the preparation of highly conductivity polymers. Thiadiazoles derivatives are structural foundation of the polymer materials. In this present work, the electronic properties of graphene nanoflakes (GNFs)-phenanthrene-1,3,4-thiadiazoles oligomers are studied and discussed. Where thiadiazoles is expanded from one to 9 unit's molecules at the structure. The energy gap, HOMO, LUMO distribution, total energy, Fermi level energy, work function, maximum wavelength absorption, vertical absorption energies, and oscillator strengths are calculated for each molecule. All calculations are carry out by usage density function theory (DFT) and depended time density function theory (TD-DFT) with the B3LYP/6-31G model in the Gaussian 09W software packages. Results show that increasing the number of monomeric units lead to great enhance in the electronic properties, which caused it decreased the band gap from 3.17 eV in the system with one unit of thiadiazole just to 1.35 eV in the system with 9 units of thiadiazole. This case is raised the value of maximum absorption wavelengths to >500 nm to give the better performance in optoelectronic and solar cell, as these structures have prime absorption bands within the solar spectrum.

Complex small-molecule architectures regulate phenotypic plasticity in a nematode.

PubMed

Bose, Neelanjan; Ogawa, Akira; von Reuss, Stephan H; Yim, Joshua J; Ragsdale, Erik J; Sommer, Ralf J; Schroeder, Frank C

2012-12-07

Chemistry the worm's way: The nematode Pristionchus pacificus constructs elaborate small molecules from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside (see scheme). These compounds act as signaling molecules to control adult phenotypic plasticity and dauer development and provide examples of modular generation of structural diversity in metazoans. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inhibiting prolyl isomerase activity by hybrid organic-inorganic molecules containing rhodium(II) fragments.

PubMed

Coughlin, Jane M; Kundu, Rituparna; Cooper, Julian C; Ball, Zachary T

2014-11-15

A small molecule containing a rhodium(II) tetracarboxylate fragment is shown to be a potent inhibitor of the prolyl isomerase FKBP12. The use of small molecules conjugates of rhodium(II) is presented as a general strategy for developing new protein inhibitors based on distinct structural and sequence features of the enzyme active site. Copyright © 2014 Elsevier Ltd. All rights reserved.

Affinity modulation of small-molecule ligands by borrowing endogenous protein surfaces

PubMed Central

Briesewitz, Roger; Ray, Gregory T.; Wandless, Thomas J.; Crabtree, Gerald R.

1999-01-01

A general strategy is described for improving the binding properties of small-molecule ligands to protein targets. A bifunctional molecule is created by chemically linking a ligand of interest to another small molecule that binds tightly to a second protein. When the ligand of interest is presented to the target protein by the second protein, additional protein–protein interactions outside of the ligand-binding sites serve either to increase or decrease the affinity of the binding event. We have applied this approach to an intractable target, the SH2 domain, and demonstrate a 3-fold enhancement over the natural peptide. This approach provides a way to modulate the potency and specificity of biologically active compounds. PMID:10051576

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.

PubMed

Ghanakota, Phani; van Vlijmen, Herman; Sherman, Woody; Beuming, Thijs

2018-04-23

The ability to target protein-protein interactions (PPIs) with small molecule inhibitors offers great promise in expanding the druggable target space and addressing a broad range of untreated diseases. However, due to their nature and function of interacting with protein partners, PPI interfaces tend to extend over large surfaces without the typical pockets of enzymes and receptors. These features present unique challenges for small molecule inhibitor design. As such, determining whether a particular PPI of interest could be pursued with a small molecule discovery strategy requires an understanding of the characteristics of the PPI interface and whether it has hotspots that can be leveraged by small molecules to achieve desired potency. Here, we assess the ability of mixed-solvent molecular dynamic (MSMD) simulations to detect hotspots at PPI interfaces. MSMD simulations using three cosolvents (acetonitrile, isopropanol, and pyrimidine) were performed on a large test set of 21 PPI targets that have been experimentally validated by small molecule inhibitors. We compare MSMD, which includes explicit solvent and full protein flexibility, to a simpler approach that does not include dynamics or explicit solvent (SiteMap) and find that MSMD simulations reveal additional information about the characteristics of these targets and the ability for small molecules to inhibit the PPI interface. In the few cases were MSMD simulations did not detect hotspots, we explore the shortcomings of this technique and propose future improvements. Finally, using Interleukin-2 as an example, we highlight the advantage of the MSMD approach for detecting transient cryptic druggable pockets that exists at PPI interfaces.

Inhibitor of PI3K/Akt Signaling Pathway Small Molecule Promotes Motor Neuron Differentiation of Human Endometrial Stem Cells Cultured on Electrospun Biocomposite Polycaprolactone/Collagen Scaffolds.

PubMed

Ebrahimi-Barough, Somayeh; Hoveizi, Elham; Yazdankhah, Meysam; Ai, Jafar; Khakbiz, Mehrdad; Faghihi, Faezeh; Tajerian, Roksana; Bayat, Neda

2017-05-01

Small molecules as useful chemical tools can affect cell differentiation and even change cell fate. It is demonstrated that LY294002, a small molecule inhibitor of phosphatidylinositol 3-kinase (PI3K)/Akt signal pathway, can inhibit proliferation and promote neuronal differentiation of mesenchymal stem cells (MSCs). The purpose of this study was to investigate the differentiation effect of Ly294002 small molecule on the human endometrial stem cells (hEnSCs) into motor neuron-like cells on polycaprolactone (PCL)/collagen scaffolds. hEnSCs were cultured in a neurogenic inductive medium containing 1 μM LY294002 on the surface of PCL/collagen electrospun fibrous scaffolds. Cell attachment and viability of cells on scaffolds were characterized by scanning electron microscope (SEM) and 3-(4,5-dimethylthiazoyl-2-yl)2,5-diphenyltetrazolium bromide (MTT) assay. The expression of neuron-specific markers was assayed by real-time PCR and immunocytochemistry analysis after 15 days post induction. Results showed that attachment and differentiation of hEnSCs into motor neuron-like cells on the scaffolds with Ly294002 small molecule were higher than that of the cells on tissue culture plates as control group. In conclusion, PCL/collagen electrospun scaffolds with Ly294002 have potential for being used in neural tissue engineering because of its bioactive and three-dimensional structure which enhances viability and differentiation of hEnSCs into neurons through inhibition of the PI3K/Akt pathway. Thus, manipulation of this pathway by small molecules can enhance neural differentiation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha

In disordered proteins we see that they are highly prevalent in biological systems. They control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27 Kip1 (p27). Moreover, two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groupsmore » of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule: disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of- principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).« less

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Widawsky, Jonathan R.

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

A RabGAP Regulates Life-Cycle Duration via Trimeric G-protein Cascades in Dictyostelium discoideum

PubMed Central

Kuwayama, Hidekazu; Miyanaga, Yukihiro; Urushihara, Hideko; Ueda, Masahiro

2013-01-01

Background The life-cycle of cellular slime molds comprises chronobiologically regulated processes. During the growth phase, the amoeboid cells proliferate at a definite rate. Upon starvation, they synthesize cAMP as both first and second messengers in signalling pathways and form aggregates, migrating slugs, and fruiting bodies, consisting of spores and stalk cells, within 24 h. In Dictyostelium discoideum, because most growth-specific events cease during development, proliferative and heterochronic mutations are not considered to be interrelated and no genetic factor governing the entire life-cycle duration has ever been identified. Methodology/Principal Findings Using yeast 2-hybrid library screening, we isolated a Dictyostelium discoideum RabGAP, Dd Rbg-3, as a candidate molecule by which the Dictyostelium Gα2 subunit directs its effects. Rab GTPase-activating protein, RabGAP, acts as a negative regulator of Rab small GTPases, which orchestrate the intracellular membrane trafficking involved in cell proliferation. Deletion mutants of Dd rbg-3 exhibited an increased growth rate and a shortened developmental period, while an overexpression mutant demonstrated the opposite effects. We also show that Dd Rbg-3 interacts with 2 Gα subunits in an activity-dependent manner in vitro. Furthermore, both human and Caenorhabditis elegans rbg-3 homologs complemented the Dd rbg-3–deletion phenotype in D. discoideum, indicating that similar pathways may be generally conserved in multicellular organisms. Conclusions/Significance Our findings suggest that Dd Rbg-3 acts as a key element regulating the duration of D. discoideum life-span potentially via trimeric G-protein cascades. PMID:24349132

Tulane/Xavier Vaccine Development/Engineering Project

DTIC Science & Technology

2009-02-01

spectroscopic studies with polar dyes (e.g. proflavine ) have verified these compounds’ ability to encapsulate and solvate small polar dye molecules in...systems. Fluorescent microscopy studies verify that they significantly enhance the transport of polar small molecules ( proflavin dye) through

Precision gap particle separator

DOEpatents

Benett, William J.; Miles, Robin; Jones, II., Leslie M.; Stockton, Cheryl

2004-06-08

A system for separating particles entrained in a fluid includes a base with a first channel and a second channel. A precision gap connects the first channel and the second channel. The precision gap is of a size that allows small particles to pass from the first channel into the second channel and prevents large particles from the first channel into the second channel. A cover is positioned over the base unit, the first channel, the precision gap, and the second channel. An port directs the fluid containing the entrained particles into the first channel. An output port directs the large particles out of the first channel. A port connected to the second channel directs the small particles out of the second channel.

Geometry, bonding and magnetism in planar triangulene graphene molecules with D3h symmetry: Zigzag Cm∗∗2+4m+1H3m+3 (m = 2, …, 15)

NASA Astrophysics Data System (ADS)

Philpott, Michael R.; Cimpoesu, Fanica; Kawazoe, Yoshiyuki

2008-12-01

Ab initio plane wave based all valence electron DFT calculations with geometry optimization are reported for the electronic structure of planar zigzag edged triangular shaped graphene molecules CH where the zigzag ring number m = 2, …, 15. The largest molecule C 286H 48 has a 3.8 nm side length and retains D3h symmetric geometry. The zone in the middle of the molecules, where the geometry and electronic properties resemble infinite single sheet graphite (graphene), expands with increasing ring number m, driving deviations in geometry, charge and spin to the perimeter. If a molecule is viewed as a set of nested triangular rings of carbon, then the zone where the lattice resembles an infinite sheet of graphene with CC = 142 pm, extends to the middle of the penultimate ring. The radial bonds joining the perimeter carbon atoms to the interior are long CC = 144 pm, except near the three apexes where the bonds are shorter. Isometric surfaces of the total charge density show that the two bonds joined at the apex have the highest valence charge. The perimeter CC bonds establish a simple pattern as the zigzag number increases, which shares some features with the zigzag edges in the D2h linear acenes C 4m+2H 2m+4 and the D6h hexangulenes CH6m but not the D6h symmetric annulenes (CH). The two CC bonds forming each apex are short (≈139 pm), next comes one long bond CC ≈ 142 pm and a middle region where all the CC bonds have length ≈141 pm. The homo-lumo gap declines from 0.53 eV at m = 2 to approximately 0.29 V at m = 15, the latter being larger than found for linear or hexagonal shaped graphenes with comparable edge lengths. Across the molecule the charge on the carbon atoms undergoes a small oscillation following the bipartite lattice. The magnitude of the charge in the same nested triangle decreases monotonically with the distance of the row from the center of the molecule. These systems are predicted to have spin polarized ground states with S = ½( m - 1), in accord with the theorems of Lieb for a bipartite lattice with unequal numbers of sub-lattice carbon atoms. The magnitude of the spin on the atoms increases monotonically from the center to the edges, this effect being greatest on the majority A-sub lattice atoms. The spins are delocalized, not confined to specific atoms as might result in geometries stabilized by islands of aromatic resonance. In the largest systems the magnetic non-bonding levels (NBL) occur as a narrowly distributed set of homos close to the Fermi level, separated from the lower lying valence bond manifold by a gap of about 1 eV. The NBL are a set of disjoint radical orbitals having charge only on atoms belonging to the A-lattice and this charge is concentrated on the perimeter and penultimate row atoms.

Mass action at the single-molecule level.

PubMed

Shon, Min Ju; Cohen, Adam E

2012-09-05

We developed a system to reversibly encapsulate small numbers of molecules in an array of nanofabricated "dimples". This system enables highly parallel, long-term, and attachment-free studies of molecular dynamics via single-molecule fluorescence. In studies of bimolecular reactions of small numbers of confined molecules, we see phenomena that, while expected from basic statistical mechanics, are not observed in bulk chemistry. Statistical fluctuations in the occupancy of sealed reaction chambers lead to steady-state fluctuations in reaction equilibria and rates. These phenomena are likely to be important whenever reactions happen in confined geometries.

Effects of Forest Gaps on Soil Properties in Castanopsis kawakamii Nature Forest.

PubMed

He, Zhongsheng; Liu, Jinfu; Su, Songjin; Zheng, Shiqun; Xu, Daowei; Wu, Zeyan; Hong, Wei; Wang, James Li-Ming

2015-01-01

The aim of this study is to analyze the effects of forest gaps on the variations of soil properties in Castanopsis kawakamii natural forest. Soil physical and chemical properties in various sizes and development stages were studied in C. kawakamii natural forest gaps. The results showed that forest gaps in various sizes and development stages could improve soil pore space structure and water characteristics, which may effectively promote the water absorbing capacity for plant root growth and play an important role in forest regeneration. Soil pore space structure and water characteristics in small gaps showed more obvious improvements, followed by the medium and large gaps. Soil pore space structure and water characteristics in the later development stage of forest gaps demonstrated more obvious improvements, followed by the early and medium development stages. The contents of hydrolysable N and available K in various sizes and development stages of forest gaps were higher than those of non-gaps, whereas the contents of total N, total P, available P, organic matter, and organic carbon were lower. The contents of total N, hydrolysable N, available K, organic matter, and organic carbon in medium gaps were higher than those of large and small gaps. The disturbance of forest gaps could improve the soils' physical and chemical properties and increase the population species' richness, which would provide an ecological basis for the species coexistence in C. kawakamii natural forest.

Persistence length of collagen molecules based on nonlocal viscoelastic model.

PubMed

Ghavanloo, Esmaeal

2017-12-01

Persistence length is one of the most interesting properties of a molecular chain, which is used to describe the stiffness of a molecule. The experimentally measured values of the persistence length of the collagen molecule are widely scattered from 14 to 180 nm. Therefore, an alternative approach is highly desirable to predict the persistence length of a molecule and also to explain the experimental results. In this paper, a nonlocal viscoelastic model is developed to obtain the persistence length of the collagen molecules in solvent. A new explicit formula is proposed for the persistence length of the molecule with the consideration of the small-scale effect, viscoelastic properties of the molecule, loading frequency, and viscosity of the solvent. The presented model indicates that there exists a range of molecule lengths in which the persistence length strongly depends on the frequency and spatial mode of applied loads, small-scale effect, and viscoelastic properties of the collagen.

Molecular gap and energy level diagram for pentacene adsorbed on filled d-band metal surfaces

NASA Astrophysics Data System (ADS)

Baldacchini, Chiara; Mariani, Carlo; Betti, Maria Grazia; Gavioli, L.; Fanetti, M.; Sancrotti, M.

2006-10-01

The authors present a combined photoemission and scanning-tunneling spectroscopy study of the filled electronic states, the molecular energy gap, and the energy level diagram of highly ordered arrays of pentacene deposited on the Cu(119) vicinal surface. The states localized at the interface are clearly singled out, comparing the results at different pentacene thicknesses and with gas-phase photoemission data. The molecular gap of 2.35eV, the hole injection barrier of 1.05eV, and the electron injection barrier of 1.30eV determine the energy level diagram of the states localized at the pentacene molecules.

Band gap opening of bilayer graphene by F4-TCNQ molecular doping and externally applied electric field.

PubMed

Tian, Xiaoqing; Xu, Jianbin; Wang, Xiaomu

2010-09-09

The band gap opening of bilayer graphene with one side surface adsorption of F4-TCNQ is reported. F4-TCNQ doped bilayer graphene shows p-type semiconductor characteristics. With a F4-TCNQ concentration of 1.3 x 10(-10) mol/cm(2), the charge transfer between each F4-TCNQ molecule and graphene is 0.45e, and the built-in electric field, E(bi), between the graphene layers could reach 0.070 V/A. The charge transfer and band gap opening of the F4-TCNQ-doped graphene can be further modulated by an externally applied electric field (E(ext)). At 0.077 V/A, the gap opening at the Dirac point (K), DeltaE(K) = 306 meV, and the band gap, E(g) = 253 meV, are around 71% and 49% larger than those of the pristine bilayer under the same E(ext).

The nanometre-scale physiology of bone: steric modelling and scanning transmission electron microscopy of collagen–mineral structure

PubMed Central

Alexander, Benjamin; Daulton, Tyrone L.; Genin, Guy M.; Lipner, Justin; Pasteris, Jill D.; Wopenka, Brigitte; Thomopoulos, Stavros

2012-01-01

The nanometre-scale structure of collagen and bioapatite within bone establishes bone's physical properties, including strength and toughness. However, the nanostructural organization within bone is not well known and is debated. Widely accepted models hypothesize that apatite mineral (‘bioapatite’) is present predominantly inside collagen fibrils: in ‘gap channels’ between abutting collagen molecules, and in ‘intermolecular spaces’ between adjacent collagen molecules. However, recent studies report evidence of substantial extrafibrillar bioapatite, challenging this hypothesis. We studied the nanostructure of bioapatite and collagen in mouse bones by scanning transmission electron microscopy (STEM) using electron energy loss spectroscopy and high-angle annular dark-field imaging. Additionally, we developed a steric model to estimate the packing density of bioapatite within gap channels. Our steric model and STEM results constrain the fraction of total bioapatite in bone that is distributed within fibrils at less than or equal to 0.42 inside gap channels and less than or equal to 0.28 inside intermolecular overlap regions. Therefore, a significant fraction of bone's bioapatite (greater than or equal to 0.3) must be external to the fibrils. Furthermore, we observe extrafibrillar bioapatite between non-mineralized collagen fibrils, suggesting that initial bioapatite nucleation and growth are not confined to the gap channels as hypothesized in some models. These results have important implications for the mechanics of partially mineralized and developing tissues. PMID:22345156

Caenorhabditis elegans chemical biology: lessons from small molecules

USDA-ARS?s Scientific Manuscript database

How can we complement Caenorhabditis elegans genomics and proteomics with a comprehensive structural and functional annotation of its metabolome? Several lines of evidence indicate that small molecules of largely undetermined structure play important roles in C. elegans biology, including key pathw...

Solution-processed small molecule:fullerene bulk-heterojunction solar cells: impedance spectroscopy deduced bulk and interfacial limits to fill-factors.

PubMed

Guerrero, Antonio; Loser, Stephen; Garcia-Belmonte, Germà; Bruns, Carson J; Smith, Jeremy; Miyauchi, Hiroyuki; Stupp, Samuel I; Bisquert, Juan; Marks, Tobin J

2013-10-21

Using impedance spectroscopy, we demonstrate that the low fill factor (FF) typically observed in small molecule solar cells is due to hindered carrier transport through the active layer and hindered charge transfer through the anode interfacial layer (IFL). By carefully tuning the active layer thickness and anode IFL in BDT(TDPP)2 solar cells, the FF is increased from 33 to 55% and the PCE from 1.9 to 3.8%. These results underscore the importance of simultaneously optimizing active layer thickness and IFL in small molecule solar cells.

Inhibitors of voltage-gated sodium channel Nav1.7: patent applications since 2010.

PubMed

Sun, Shaoyi; Cohen, Charles J; Dehnhardt, Christoph M

2014-09-01

There has been intense interest in developing inhibitors of the sodium channel Nav1.7 because genetic studies have established very strong validation for the efficacy to alleviate both inflammatory and neuropathic pain. This review summarizes patent applications targeting Nav1.7 since 2010 until May, 2014. We have classified the patents into three categories as follows: small molecules with well-defined molecular selectivity among sodium channel isoforms; biologicals with well-defined molecular selectivity; and, small molecules that inhibit Nav1.7 with unknown molecular selectivity. Most of the review is dedicated to small molecule selective compounds.

The Evolution of Design

ERIC Educational Resources Information Center

Stebbins, G. Ledyard

1973-01-01

Describes the basic logic behind the modern view of evolution theory. Despite gaps in fossil records, evidence is indicative of the origin of life from nonliving molecules and evolution of higher forms of life from simpler forms. (PS)

Photobleaching dynamics in small molecule vs.  polymer organic photovoltaic blends with 1,7-bis-trifluoromethylfullerene

DOE PAGES

Garner, Logan E.; Nellissery Viswanathan, Vinila; Arias, Dylan H.; ...

2018-02-27

Two organic photovoltaic (OPV) donor materials (one polymer and one small molecule) are synthesized from the same constituent building blocks, namely thiophene units, cyclopentathiophene dione (CTD), and cyclopentadithiophene (CPDT). Photobleaching dynamics of these donor materials are then studied under white light illumination in air with blends of PC 70BM and the bistrifluoromethylfullerene 1,7-C 60(CF 3) 2. For both the polymer and small molecule blends, C 60(CF 3) 2 stabilizes the initial rate of photobleaching by a factor of 15 relative to PC70BM. However, once the small molecule:C 60(CF 3) 2 blend bleaches to ~80% of its initial optical density, themore » rate of photobleaching dramatically accelerates, which is not observed in the analagous polymer blend. We probe that phenomenon using time-resovled photoluminescence (TRPL) to measure PL quenching efficiencies at defined intervals during the photobleaching experiments. The data indicates the small molecule donor and C 60(CF 3) 2 acceptor significantly de-mix with time, after which the blend begins to bleach at approximately the same rate as the neat donor sample. The work suggests that perfluoroalkylfullerenes have great potential to stabilize certain OPV active layers toward photodegradation, provided their morphology is stable.« less

Photobleaching dynamics in small molecule vs.  polymer organic photovoltaic blends with 1,7-bis-trifluoromethylfullerene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garner, Logan E.; Nellissery Viswanathan, Vinila; Arias, Dylan H.

Two organic photovoltaic (OPV) donor materials (one polymer and one small molecule) are synthesized from the same constituent building blocks, namely thiophene units, cyclopentathiophene dione (CTD), and cyclopentadithiophene (CPDT). Photobleaching dynamics of these donor materials are then studied under white light illumination in air with blends of PC 70BM and the bistrifluoromethylfullerene 1,7-C 60(CF 3) 2. For both the polymer and small molecule blends, C 60(CF 3) 2 stabilizes the initial rate of photobleaching by a factor of 15 relative to PC70BM. However, once the small molecule:C 60(CF 3) 2 blend bleaches to ~80% of its initial optical density, themore » rate of photobleaching dramatically accelerates, which is not observed in the analagous polymer blend. We probe that phenomenon using time-resovled photoluminescence (TRPL) to measure PL quenching efficiencies at defined intervals during the photobleaching experiments. The data indicates the small molecule donor and C 60(CF 3) 2 acceptor significantly de-mix with time, after which the blend begins to bleach at approximately the same rate as the neat donor sample. The work suggests that perfluoroalkylfullerenes have great potential to stabilize certain OPV active layers toward photodegradation, provided their morphology is stable.« less

A Potent and Selective Quinoxalinone-Based STK33 Inhibitor Does Not Show Synthetic Lethality in KRAS-Dependent Cells

PubMed Central

2012-01-01

The KRAS oncogene is found in up to 30% of all human tumors. In 2009, RNAi experiments revealed that lowering mRNA levels of a transcript encoding the serine/threonine kinase STK33 was selectively toxic to KRAS-dependent cancer cell lines, suggesting that small-molecule inhibitors of STK33 might selectively target KRAS-dependent cancers. To test this hypothesis, we initiated a high-throughput screen using compounds in the Molecular Libraries Small Molecule Repository (MLSMR). Several hits were identified, and one of these, a quinoxalinone derivative, was optimized. Extensive SAR studies were performed and led to the chemical probe ML281 that showed low nanomolar inhibition of purified recombinant STK33 and a distinct selectivity profile as compared to other STK33 inhibitors that were reported in the course of these studies. Even at the highest concentration tested (10 μM), ML281 had no effect on the viability of KRAS-dependent cancer cells. These results are consistent with other recent reports using small-molecule STK33 inhibitors. Small molecules having different chemical structures and kinase-selectivity profiles are needed to fully understand the role of STK33 in KRAS-dependent cancers. In this regard, ML281 is a valuable addition to small-molecule probes of STK33. PMID:23256033

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS

NASA Astrophysics Data System (ADS)

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-01-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H]-) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. [Figure not available: see fulltext.

Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines

PubMed Central

Zhang, Xinyuan; Zheng, Nan

2008-01-01

Cell-based molecular transport simulations are being developed to facilitate exploratory cheminformatic analysis of virtual libraries of small drug-like molecules. For this purpose, mathematical models of single cells are built from equations capturing the transport of small molecules across membranes. In turn, physicochemical properties of small molecules can be used as input to simulate intracellular drug distribution, through time. Here, with mathematical equations and biological parameters adjusted so as to mimic a leukocyte in the blood, simulations were performed to analyze steady state, relative accumulation of small molecules in lysosomes, mitochondria, and cytosol of this target cell, in the presence of a homogenous extracellular drug concentration. Similarly, with equations and parameters set to mimic an intestinal epithelial cell, simulations were also performed to analyze steady state, relative distribution and transcellular permeability in this non-target cell, in the presence of an apical-to-basolateral concentration gradient. With a test set of ninety-nine monobasic amines gathered from the scientific literature, simulation results helped analyze relationships between the chemical diversity of these molecules and their intracellular distributions. Electronic supplementary material The online version of this article (doi:10.1007/s10822-008-9194-7) contains supplementary material, which is available to authorized users. PMID:18338229

Signal-enhancer molecules encapsulated liposome as a valuable sensing and amplification platform combining the aptasensor for ultrasensitive ECL immunoassay.

PubMed

Mao, Li; Yuan, Ruo; Chai, Yaqin; Zhuo, Ying; Xiang, Yun

2011-06-15

An innovatory ECL immunoassay strategy was proposed to detect the newly developing heart failure biomarker N-terminal pro-brain natriuretic peptide (NT-proBNP). Firstly, this strategy used small molecules encapsulated liposome as immune label to construct a sandwich immune sensing platform for NT-proBNP. Then the ECL aptasensor was prepared to collect and detect the small molecules released from the liposome. Finally, based on the ECL signal changes caused by the small molecules, the ECL signal indirectly reflected the level of NT-proBNP antigen. In this experiment, the cocaine was chosen as the proper small molecule that can act as signal-enhancer to enhance the ECL of Ru(bpy)(3)(2+). The cocaine-encapsulated liposomes were successfully characterized by TEM. The quantificational calculation proved the ∼5.3×10(3) cocaine molecules per liposome enough to perform the assignment of signal amplification. The cocaine-binding ECL aptasensor further promoted the work aimed at amplifying signal. The performance of NT-proBNP assay by the proposed strategy exhibited high sensitivity and high specificities with a linear relationship over 0.01-500 ng mL(-1) range, and a detection limit down to 0.77 pg mL(-1). Copyright © 2011 Elsevier B.V. All rights reserved.

Patterns of Change in U.S. Gender Achievement Gaps during Elementary and Middle School

ERIC Educational Resources Information Center

Fahle, Erin

2016-01-01

Research on gender achievement gaps shows they exist, and are largest in the tails of the distribution, starting as early as Kindergarten and persisting through eighth grade. In mathematics, studies find small average gender achievement gaps and larger systematically male-favoring gaps among the highest achieving students. This paper seeks to…

Giant Enhancement in Radiative Heat Transfer in Sub-30 nm Gaps of Plane Parallel Surfaces.

PubMed

Fiorino, Anthony; Thompson, Dakotah; Zhu, Linxiao; Song, Bai; Reddy, Pramod; Meyhofer, Edgar

2018-06-13

Radiative heat transfer rates that exceed the blackbody limit by several orders of magnitude are expected when the gap size between plane parallel surfaces is reduced to the nanoscale. To date, experiments have only realized enhancements of ∼100 fold as the smallest gap sizes in radiative heat transfer studies have been limited to ∼50 nm by device curvature and particle contamination. Here, we report a 1,200-fold enhancement with respect to the far-field value in the radiative heat flux between parallel planar silica surfaces separated by gaps as small as ∼25 nm. Achieving such small gap sizes and the resultant dramatic enhancement in near-field energy flux is critical to achieve a number of novel near-field based nanoscale energy conversion systems that have been theoretically predicted but remain experimentally unverified.

Groundlayer vegetation gradients across oak woodland canopy gaps

USGS Publications Warehouse

Pavlovic, N.B.; Grundel, R.; Sluis, W.

2006-01-01

Frequency of groundlayer plants was measured across oak woodland canopy gaps at three sites in northwest Indiana to examine how vegetation varied with gap size, direction along the gap edge, and microhabitat. Microhabitats were defined as under the canopy adjacent to the gap, along the gap edge, and within the gap. Gap-sites consisted of gaps plus adjacent tree canopy. Gaps were classified as small (16 ± 1 m2), medium (97 ± 8), and large (310 ± 32). Neither richness nor diversity differed among microhabitats, gap sizes, or edges. Similarity between microhabitats wthin a gap-site increased as the distance between plots decreased and as the difference in PAR decreased, the latter explaining twice the variation in percent dissimilarity compared to Mg concentration, A horizon depth, and litter cover. Diervilla lonicera, Frageria virginiana, Helianthus divaricatus, Polygonatum pubescens, Quercus velutina, Smilacena stellata, and Tradescantia ohiensis decreased, whileTephrosia virginiana and legumes increased in frequency, from canopy to gap, and C4 grasses peaked at the gap edge, independent of gap size. Additional species frequency varied across the microhabitat gradient within specific sites. Sorghastrum nutans was three times more frequent in gaps at large sites than elsewhere. The vegetation in medium-sized gap-sites was more variable than within small and large gap-sites, suggesting greater environmental heterogeneity at that scale. Within gap-sites, vegetation was more heterogeneous within edges and canopies than in gaps. Edges were more similar in composition to gaps than to canopy groundlayer within gap-sites. Few species varied significantly in frequency around the gap edge. The oak woodland groundlayer on sandy substrates can be characterized as a mosaic of forb dominated vegetation that varies across light gradients associated with canopy gaps, transitioning to islands of grassland vegetation when gaps exceed 160 m2.

Conformational, spectroscopic and nonlinear optical properties of biologically active N,N-dimethyltryptamine molecule: A theoretical study

NASA Astrophysics Data System (ADS)

Öner, Nazmiye; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

2014-12-01

The effective psychoactive properties of N,N-dimethyltryptamine (DMT) known as the near-death molecule have encouraged the imagination of many research disciplines for several decades. Although there is no theoretical study, a number of paper composed by experimental techniques have been reported for DMT molecule. In this study, the molecular modeling of DMT was carried out using B3LYP and HSEh1PBE levels of density functional theory (DFT). Our calculations showed that the energy gap between HOMO and LUMO is low, demonstrating that DMT is a biologically active molecule. Large hyperconjugation interaction energies imply that molecular charge transfer occurs in DMT. Moreover, NLO analysis indicates that DMT can be used an effective NLO material.

Theoretical study on adsorption and dissociation of NO2 molecules on BNNT surface

NASA Astrophysics Data System (ADS)

Singla, Preeti; Singhal, Sonal; Goel, Neetu

2013-10-01

The adsorption of NO2 molecules on (8,0) zigzag single-walled boron nitride nanotube surface is investigated using density functional theory calculations. Two interaction modes, nitro (interacting atom is N) and nitrite (O interacts with BNNT) have been studied with increase in number of NO2 molecules. The adsorption of single NO2 molecule in both configurations is observed to be exothermic and physical in nature. However, in nitrite configuration, NO2 molecules are chemisorbed on the surface leading to the dissociation of NO2 molecules into NO and O. The density of states, natural bond orbital analysis and frontier orbital pictures provide rational understanding of the charge transfer involved in the process and predict significant enhancement in the conductivity of the BNNT after NO2 adsorption. The DFT calculations show that NO2 adsorption introduces new impurity states in the band gap of bare BNNT and expand their applications as NO2 molecule gas sensor and catalytic surface for Nsbnd O dissociation depending upon the mode of adsorption.