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Gemin Fang, Oliver Seitz
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached via covalent bonds to an oligonucleotide probe. However, the additional conjugation step increases costs. Herein we introduce a method that avoids the requirement for the preparation of fluorescence labeled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid probes to form a bipartite tetracysteine motif which binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH...
November 24, 2016: Chembiochem: a European Journal of Chemical Biology
Wenxing Jin, Yi Wang, Chao-Pei Liu, Na Yang, Mingliang Jin, Yao Cong, Mingzhu Wang, Rui-Ming Xu
Assembly of the spliceosomal small nuclear ribonucleoparticle (snRNP) core requires the participation of the multisubunit SMN (survival of motor neuron) complex, which contains SMN and several Gemin proteins. The SMN and Gemin2 subunits directly bind Sm proteins, and Gemin5 is required for snRNP biogenesis and has been implicated in snRNA recognition. The RNA sequence required for snRNP assembly includes the Sm site and an adjacent 3' stem-loop, but a precise understanding of Gemin5's RNA-binding specificity is lacking...
November 1, 2016: Genes & Development
Peter A Limacher
A new truncation scheme for non-orthogonal antisymmetrized products of interacting geminals (APIG) is introduced based on antisymmetrized products of strongly orthogonal geminals (APSG). This wavefunction hierarchy of interacting geminals (IG) allows us to gradually increase the accuracy at which the ground state of a seniority-zero Hamiltonian can be estimated, ranging from APSG up to approximation-free APIG. Mathematical expressions for the lowest four orders (IG0, IG1, IG2, and IG3) are given explicitly and the computational cost to evaluate their transition density matrix is verified to scale only cubically with system size...
November 21, 2016: Journal of Chemical Physics
Diana Yepes, Pablo Jaque, Israel Fernández
H2 activation mediated by geminal aminoborane-based frustrated Lewis pairs (FLPs; R2 N-CH2 -BR'2 ) has been computationally explored within the density functional theory framework. It is found that the activation barrier of this process as well as the geometry of the corresponding transition states strongly depend on the nature of the substituents directly attached either to the acidic or the basic centers of the FLPs. The physical factors controlling the whole activation path are quantitatively described in detail by means of the activation strain model of reactivity combined with the energy decomposition analysis method...
November 16, 2016: Chemistry: a European Journal
Giuseppina Turco, Bettina Braun
The present study investigates non-local temporal adjustments before an upcoming length contrast in Italian minimal pairs that differ only in the length of the medial consonant (e.g., geminate word palla "ball" vs singleton word pala "shovel"). This contrast is reportedly signaled by the duration of the singleton/geminate consonant and of the preceding vowel. Here, it is shown that the duration adjustment extends further to the word-initial consonant, e.g., the [p] in palla is significantly longer than that in pala (experiment 1)...
October 2016: Journal of the Acoustical Society of America
Martin Stolterfoht, Ardalan Armin, Bronson Philippa, Dieter Neher
The competition between charge extraction and non-geminate recombination critically determines the current-voltage characteristics of organic solar cells (OSCs) and their fill factor. As a measure of this competition, several figures of merit (FOMs) have been put forward, however, the impact of space charge effects has been either neglected, or is not specifically addressed. Here we revisit recently reported FOMs and discuss the role of space charge effects on the interplay between recombination and extraction...
October 28, 2016: Journal of Physical Chemistry Letters
Kenji Matsumoto, Kosuke Hayashi, Kaoru Murata-Hirai, Masashi Iwasaki, Haruki Okamura, Nagahiro Minato, Craig T Morita, Yoshimasa Tanaka
Nitrogen-containing bisphosphonates have antitumor activity in certain breast cancer and myeloma patients. However, these drugs have limited oral absorption, tumor cell entry and activity, and cause bone side effects. The potencies of phosphorylated antiviral drugs have been increased by administering them as prodrugs, in which the negative charges on the phosphate moieties are masked to make them lipophilic. We synthesized heterocyclic bisphosphonate (BP) prodrugs in which the phosphonate moieties are derivatized with pivaloyloxymethyl (pivoxil) groups and that lack the hydroxy "bone hook" on the geminal carbon...
October 27, 2016: ChemMedChem
Cole M Johnson, Alexander E Doran, Jinmei Zhang, Edward F Valeev, So Hirata
A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method...
October 21, 2016: Journal of Chemical Physics
Denis Bokhan, Dmitrii N Trubnikov, Ajith Perera, Rodney J Bartlett
A method of calculation of static polarizabilities with wavefunctions, corresponding to linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] model, has been formulated and implemented. For the proper description of the response of system on applied electric field, modified ansatz is introduced for geminal part of cluster operators. Such extension of CCSD(F12) model provides balanced description of both perturbed and unperturbed wave functions, what leads to the increase of the accuracy of target polarizabilities...
October 7, 2016: Journal of Chemical Physics
MingBing Zhong, Song Sun, Jiang Cheng, Ying Shao
An iron-catalyzed intermolecular [4+2] cyclization of arylnitrones with geminal-substituted vinyl acetates was developed for the synthesis of 2,4-disubstituted quinolines in moderate to good yields with good functional group compatibilities. Preliminary mechanistic studies suggest a plausible iron-catalyzed C-H activation process under external-oxidant-free conditions.
October 21, 2016: Journal of Organic Chemistry
Pablo Arturo Fernández Garrillo, Lukasz Borowik, Florent Caffy, Renaud Demadrille, Benjamin Grevin
Investigating the photo-carrier dynamics in nanostructured and heterogeneous energy materials is of crucial importance from both fundamental and technological points of view. Here, we demonstrate how non-contact atomic force microscopy combined with Kelvin Probe Force Microscopy under frequency modulated illumination can be used to simultaneously image the surface photo-potential dynamics at different timescales with a sub-10 nm lateral resolution. The basic principle of the method consists in the acquisition of spectroscopic curves of the surface potential as a function of the illumination frequency modulation on a two dimensional grid...
October 20, 2016: ACS Applied Materials & Interfaces
Yujing Zhou, Yan Zhang, Jianbo Wang
A general approach towards diverse fluorinated phosphonates via geminal difunctionalization reactions of α-diazo arylmethylphosphonates is described. The diazo functionality (RR'C[double bond, length as m-dash]N2) is successfully converted to RR'CF2, RR'CHF, RR'CFBr or RR'CFNR''2 groups by employing different fluorination reagents. A variety of fluorinated organophosphorus compounds were readily accessed in good to excellent yields from a common type of precursor.
October 19, 2016: Organic & Biomolecular Chemistry
Hui Yang, Huabo Duan, Xu Wu, Min Wang, Ting Chen, Fanghui Liu, Shizhe Huang, Wei Zhang, Gang Chen, Danfeng Yu, Jinben Wang
The adsorption processes of a geminized amphiphilic polyelectrolyte, comprising double elementary charges and double hydrophobic tails in each repeat unit (denoted as PAGC8), was investigated and characterized by means of quartz crystal microbalance with dissipation (QCM-D), ellipsometry, and atomic force microscopy (AFM). By comparison, the self-assembly behaviors of a traditional polyelectrolyte without hydrophobic chains (denoted as PASC1), and an amphiphilic polyelectrolyte with a single hydrophilic head group and hydrophobic tail in each repeat unit (denoted as PASC8) at the solid/liquid interface, were also investigated in parallel...
October 18, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Chandresakaran Prathipa, Lakshminarayanan Akilandeswari
There are eight possible pathways for the iron-tricarbonyl-assisted thermal electrocyclic ring opening of fluorocyclobutene due to variations in the orientation of the binding of Fe(CO)3 relative to the fluorine substituent (R1 or R2), stereoselectivity (conrotatory or disrotatory, i.e., C or D), and the torquoselectivity of fluorine (inward-facing or outward-facing, i.e., in or out). A density functional study revealed that the energetically favored pathway is R1 Din. Not only is the D mode favored energetically, but the in configuration was observed to be the lowest-lying mode of R1, despite the general tendency of fluorine substituents to prefer an out configuration...
November 2016: Journal of Molecular Modeling
Benjamin Schumann, Sharavathi G Parameswarappa, Marilda P Lisboa, Naresh Kottari, Fabio Guidetti, Claney L Pereira, Peter H Seeberger
The glycosylation reaction is the key transformation in oligosaccharide synthesis, but it is still difficult to control in many cases. Stereocontrol during cis-glycosidic linkage formation relies almost exclusively on tuning the glycosylating agent or the reaction conditions. Herein, we use nucleophile-directed stereocontrol to manipulate the stereoselectivity of glycosylation reactions. Placing two fluorine atoms in close proximity to the hydroxy group of an aliphatic amino alcohol lowers the oxygen nucleophilicity and reverses the stereoselectivity of glycosylations to preferentially form the desired cis-glycosides with a broad set of substrates...
October 13, 2016: Angewandte Chemie
Safa Shoaee, Shengqiang Fan, Paul L Burn, Paul E Shaw
Fluorescence-based detection of explosive analytes requires an understanding of the nature of the excited state responsible for the luminescence response of a sensing material. Many measurements are carried out to elucidate the fundamental photophysical properties of an emissive material in solution. However, simple transfer of the understanding gained from the solution measurements to the solid-state can lead to errors. This is in part due to the absence of inter-molecular interactions of the chromophores in solution, which are present in the solid-state...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Jonathan Coronel-León, Aurora Pinazo, Lourdes Pérez, Mª José Espuny, Ana Mª Marqués, Angeles Manresa
Recently it has been demonstrated that catanionic mixtures of oppositely charged surfactants have improved physicochemical-biological properties compared to the individual components. Isotherms of mixtures of an anionic biosurfactant (lichenysin) and a cationic aminoacid surfactant (C3(LA)2) indicate a strong interaction suggesting the formation of a new "pseudo-surfactant". The antimicrobial properties of the mixture lichenysin and C3(LA)2 M80:20, indicate a synergistic effect of the components. The mechanism of action on the bacterial envelope was assessed by flow cytometry and Transmission Electron Microscopy...
October 4, 2016: Colloids and Surfaces. B, Biointerfaces
Arnau Vilà, Miguel González
The influence of the mass in the photodissociation dynamics of a homonuclear diatomic molecule (X2), embedded in a superfluid helium nanodroplet (T = 0.37 K) of 300 atoms, has been investigated using a hybrid quantum dynamics method recently proposed by us. Several hypothetical isotopic variants of Cl2 have been examined in order to make possible the analysis of a wide diversity of masses (mX: 0.25mCl-1.50mCl). This is probably the first time that this problem has been considered theoretically. The photodissociation mechanism of X2(B) is very similar to that of Cl2(B) and the efficiency of the X2-helium energy exchange mechanism can be so great that it leads to the full and partial (≈86%) geminate recombination for the lower masses explored (mX = 0...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Ekaterina A Lukina, Alexander A Popov, Mikhail N Uvarov, Elizaveta A Suturina, Edward J Reijerse, Leonid V Kulik
A composite material of semiconducting polymer P3HT and fullerene derivative PC70BM was studied by means of electron spin echo (ESE) spectroscopy. The out-of-phase ESE signal was observed under laser irradiation of the composite at low temperature. We assume that during the charge separation process firstly the spin-correlated radical pairs in the singlet-polarized spin state are formed, and then the net polarization of radical pairs arises due to spin evolution. Both types of polarizations contribute to the out-of-phase ESE signal in the case of non-ideal microwave pulses...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Takuro Matsumoto, Ayaka Ono, Takahiro Ichikawa, Takashi Kato, Hiroyuki Ohno
Gemini amphiphilic zwitterions exhibit thermotropic bicontinuous cubic liquid-crystalline phases having a 3D continuous ionic domain. Incorporation of an acid into the materials led to the creation of novel electrolytes transporting protons efficiently through the 3D continuous domain.
October 6, 2016: Chemical Communications: Chem Comm
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