Single Acceptor Research Articles

4-Carbamoylpiperidinium phenylacetate hemihydrate

The asymmetric unit of the title compound, C6H13N2O+·C8H7O2 −·0.5H2O, comprises two isonipecotamide cations, two phenyl­acetate anions and a water mol­ecule of solvation. The hydrogen-bonding environments for both sets of ion pairs are essentially identical with the piperidinium and amide ‘ends’ of each cation involved in lateral heteromolecular hydrogen-bonded cyclic N—H⋯O associations [graph set R 2 2(11)] which incorporate a single carboxyl O-atom acceptor. These cyclic motifs enclose larger R 5 5(21) cyclic systems, forming sheet substructures which lie parallel to (101) and are linked across b by the single water mol­ecule via water O—H⋯Oc (c = carboxylate) associations, giving a duplex-sheet structure.

Excess Electron and Lithium Atom Solvation in Water Clusters at Finite Temperature: An ab Initio Molecular Dynamics Study of the Structural, Spectral, and Dynamical Behavior of (H2O)6− and Li(H2O)6

The roles of hydrogen bonds in the solvation of an excess electron and a lithium atom in water hexamer cluster at 150 K have been studied by means of ab initio molecular dynamics simulations. It is found that the hydrogen bonded structures of (H(2)O)(6)(-) and Li(H(2)O)(6) clusters are very different from each other and they dynamically evolve from one conformer to other along their simulation trajectories. The populations of the single acceptor, double acceptor, and free type water molecules are found to be significantly high unlike that in pure water clusters. Free hydrogens of these type of water molecules primarily capture the unbound electron density in these clusters. It is found that the binding motifs of the free electron evolve with time and the vertical detachment energy of (H(2)O)(6)(-) and vertical ionization energy of Li(H(2)O)(6) also change with time. Assignments of the observed peaks in vibrational power spectra are done, and we found direct correlations between the time-averaged population of water molecules in different hydrogen bonding states and the spectral features. The dynamical aspects of these clusters have also been studied through calculations of time correlations of instantaneous stretch frequencies of OH modes which are obtained from the simulation trajectories through a time series analysis.

Dual-Channel Single-Molecule Fluorescence Resonance Energy Transfer to Establish Distance Parameters for RNA Nanoparticles

The increasing interest in RNA nanotechnology and the demonstrated feasibility of using RNA nanoparticles as therapeutics have prompted the need for imaging systems with nanometer-scale resolution for RNA studies. Phi29 dimeric pRNAs can serve as building blocks in assembly into the hexameric ring of the nanomotors, as modules of RNA nanoparciles, and as vehicles for specific delivery of therapeutics to cancers or viral infected cells. The understanding of the 3D structure of this novel RNA dimeric particle is fundamentally and practically important. Although a 3D model of pRNA dimer has been proposed based on biochemical analysis, no distance measurements or X-ray diffraction data have been reported. Here we evaluated the application of our customized single-molecule dual-viewing system for distance measurement within pRNA dimers using single-molecule Fluorescence Resonance Energy Transfer (smFRET). Ten pRNA monomers labeled with single donor or acceptor fluorophores at various locations were constructed and eight dimers were assembled. smFRET signals were detected for six dimers. The tethered arm sizes of the fluorophores were estimated empirically from dual-labeled RNA/DNA standards. The distances between donor and acceptor were calculated and used as distance parameters to assess and refine the previously reported 3D model of the pRNA dimer. Distances between nucleotides in pRNA dimers were found to be different from those of the dimers bound to procapsid, suggesting a conformational change of the pRNA dimer upon binding to the procapsid.

Effect of Source/Drain Doping Gradient on Threshold Voltage Variation in Double-Gate Fin Field Effect Transistors as Determined by Discrete Random Doping

We present a numerical simulation and physical analysis of how a single dopant in the channel region effects the variation of threshold voltage ΔVth in highly scaled (gate length = 16 nm) and undoped double-gate fin field effect transistors. The presence of a single contaminant dopant in an undoped channel with an abrupt source/drain (S/D) doping gradient can cause a severe change in ΔVth (140 mV owing to a single acceptor; 100 mV owing to a single donor). To effectively suppress this severe variation, we suggest S/D doping gradient engineering to make the lateral straggle of S/D doping (σS/D) larger than 2 nm to minimize ΔVth. The distribution of Vth is also estimated by three-dimensional simulation using the position of the dopant.

ChemInform Abstract: Arsenic Compounds from the Kidney of the Giant Clam Tridacna maxima: Isolation and Identification of an Arsenic-Containing Nucleoside.

The kidney of the giant clam Tridacna maxima contains algal arsenic compounds, probably as a consequence of the clam's symbiotic relationship with unicellular algae (zooxanthallae). Extraction of Tridacna kidneys yielded three novel arsenic compounds, N-(5′-deoxy-5′-dimethylarsinoyl-β-D-ribosyloxycarbonyl)glycine 5, (2S)-3-(5′-deoxy-5′-dimethylarsinoyl-β-D-ribosyloxy)-2-hydroxypropanoic acid 4a, and (2R)-3-(5′-deoxy-5′-dimethylarsinoyl-β-D-ribosyloxy)-2-hydroxypropanoic acid 4b, in addition to four previously reported dimethylarsinoylribosides. The structures of the three new Compounds were assigned chiefly from NMR data, and those for compounds 4a and 4b were confirmed by synthesis. Extraction of a second batch of Tridacna kidneys gave, in addition to compounds identified in the first extraction, (2S)-3-[(5′-deoxy-5′-trimethylarsonio-β-D-ribosyloxy)-2-hydroxypropyl]sulfate 18 and two novel compounds: an arsenic-containing nucleoside, 9-(5′-deoxy-5′-dimethylarsinoyl)-9H-adenosine 16 and N-[4-(dimethylarsinoyl)butanoyl]taurine 21. Syntheses of compounds 16 and 21 are reported. The presence of the nucleoside 16 in Tridacna, as a consequence of algal metabolism, supports a proposed pathway for the biogenesis of arsenic-containing ribosides by algae involving methylation and adenosylation by S-adenosylmethionine. A biogenetic pathway for compound 21 involving donation of the 3-amino-3-carboxypropyl moiety of S-adenosylmethionine is also proposed. The presence of both compounds 16 and 21 in Tridacna may represent the first example of donation, by S-adenosylmethionine, of all three of its alkyl groups to a single acceptor (arsenic) within one organism.

Oligomeric Size of the M2 Muscarinic Receptor in Live Cells as Determined by Quantitative Fluorescence Resonance Energy Transfer

Fluorescence resonance energy transfer (FRET), measured by fluorescence intensity-based microscopy and fluorescence lifetime imaging, has been used to estimate the size of oligomers formed by the M(2) muscarinic cholinergic receptor. The approach is based on the relationship between the apparent FRET efficiency within an oligomer of specified size (n) and the pairwise FRET efficiency between a single donor and a single acceptor (E). The M(2) receptor was fused at the N terminus to enhanced green or yellow fluorescent protein and expressed in Chinese hamster ovary cells. Emission spectra were analyzed by spectral deconvolution, and apparent efficiencies were estimated by donor-dequenching and acceptor-sensitized emission at different ratios of enhanced yellow fluorescent protein-M(2) receptor to enhanced green fluorescent protein-M(2) receptor. The data were interpreted in terms of a model that considers all combinations of donor and acceptor within a specified oligomer to obtain fitted values of E as follows: n = 2, 0.495 +/- 0.019; n = 4, 0.202 +/- 0.010; n = 6, 0.128 +/- 0.006; n = 8, 0.093 +/- 0.005. The pairwise FRET efficiency determined independently by fluorescence lifetime imaging was 0.20-0.24, identifying the M(2) receptor as a tetramer. The strategy described here yields an explicit estimate of oligomeric size on the basis of fluorescence properties alone. Its broader application could resolve the general question of whether G protein-coupled receptors exist as dimers or larger oligomers. The size of an oligomer has functional implications, and such information can be expected to contribute to an understanding of the signaling process.

Synthesis and Structural Characterization of Diisopropylammonium Trifluoroacetate and Diisoproplyammonium Pentafluoropropionate

Diisopropylammonium trifluoroacetate ({[iPr2NH2][CF3COO]}; dip tfa; 1) and diisopropylammonium pentafluoropropionate ({[iPr2NH2][C2F5COO]}; dip pfp; 2) have been synthesized and structurally characterized by X-ray diffraction and spectroscopic methods. Both compounds form hydrogen-bonded cyclic dimers (Etter symbol: R4 4 (12)) in the solid state. The asymmetric unit of 1 contains one trifluoroacetate anion and one dip cation in the centrosymmetric space group Pī. The asymmetric unit of 2 consists of two crystallographically independent pentafluoropropionate anions and two independent dip cations forming dimers in the form of rings, both lying around centers of symmetry in the space group Pī. In dip tfa and dip pfp the cations act as double hydrogen bond donors, and each of the two oxygen atoms of the carboxyl group are single hydrogen bond acceptors. The donor acceptor distances of the N-H...O hydrogen bonds are within the expected range for medium strong hydrogen bonds. The quasi-molecular cyclic dimers are connected with neighboring units only by van der Waals interactions.

Tris(1,10-phenanthroline-κ2N,N′)cadmium(II) bis(perchlorate) 3.5-hydrate: a water chain stabilized by perchlorate anions

The title compound, [Cd(C(12)H(8)N(2))(3)](ClO(4))(2).3.5H(2)O, contains a cross-shaped one-dimensional channel along the c axis which encapsulates an ordered water chain. This water chain features a centrosymmetric cyclic water hexamer unit with a chair-like conformation. Neighbouring hexamers are linked by bridging water molecules. The host perchlorate anions recognize and stabilize the guest water chain via three kinds of hydrogen-bond patterns, leading to the formation of a complex one-dimensional {[(H(2)O)(7)(ClO(4))(4)](4-)}(n) anionic chain. One perchlorate acts as a single hydrogen-bond acceptor dangling on the chain, the second perchlorate on the chain serves as a double hydrogen-bond acceptor for only one water molecule to form an R(2)(2)(6) ring, where both entities lie on a twofold axis, while the third perchlorate, which also lies on a twofold axis, accepts two hydrogen bonds from two equivalent water molecules and is involved in the construction of an R(6)(5)(14) ring.

The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy

In this work, the Raman spectra of aqueous C(12)E(5) solutions are recorded and utilized to demonstrate the existence of single donator-single acceptor (DA) hydrogen bonding in water. From Raman OH stretching bands of aqueous C(12)E(5) solutions, the relative intensity of 3430 cm(-1) subband increases with C(12)E(5) concentrations. For confined water, the DA hydrogen bonding can be expected to be the important hydrogen bonding species. Therefore, the 3430 cm(-1) component can be ascribed to OH vibration engaged in DA hydrogen bonding. This is in agreement with our recent explanation on Raman OH stretching band of water. For water at ambient conditions, the double donor-double acceptor (DDAA) and DA should be the dominant hydrogen bonding species, the ratio of DDAA to DA can be approximately to be 0.75:1, and the mean hydrogen bonding can be determined to be 2.75.

Irregular Excess Energy Transfer Observed with a Cerulean Donor and Multiple Venus FRET Acceptors

Forster resonance energy transfer (FRET) is a mechanism where energy is transferred from an excited donor fluorophore to adjacent chromophores via non-radiative dipole-dipole interactions. FRET theory primarily considers the interactions of a single donor-acceptor pair. Unfortunately, it is rarely known if only a single acceptor is present in a molecular complex. Thus, the use of FRET as a tool for measuring protein-protein interactions inside living cells requires an understanding of how FRET changes with multiple acceptors. When multiple FRET acceptors are present it is assumed that a quantum of energy is either released from the donor, or transferred to only one of the acceptors present. The rate of energy transfer between the donor and each specific acceptor (kDA) can be measured in the absence of other acceptors, and these individual transfer rates can be used to predict the ensemble FRET efficiency. The generality of this approach was tested by measuring the ensemble FRET efficiency in two constructs, each containing a single fluorescent-protein donor (Cerulean) and either two or three acceptors (Venus). FRET transfer rates between individual donor-acceptor pairs were measured by systematically introducing point mutations to eliminate the chromophores of the other acceptors. We find that the amount of FRET with multiple acceptors is significantly greater than predicted by the sum of the individual transfer rates. We conclude that either an additional energy transfer pathway exists when multiple acceptors are present, or that a theoretical assumption that the prediction calculation is based on is incorrect. These possibilities will be discussed.

Dual-Channel Single-Molecule Imaging of pRNA on phi29 DNA-Packaging Motor

Bacteriophage phi29 DNA-packaging motor is geared by six packaging RNAs (pRNA). The pRNA molecules have been reported to serve as building blocks in RNA nanotechnology, and as vehicles for specific delivery of therapeutics to treat cancers and viral infections. The understanding of the 3D structure of pRNA and its location and positioning on the motor are both fundamentally and practically important. A customized single-molecule dual-color imaging system has been constructed to study the structures of pRNA molecules. The system is the combination of a low-temperature (−80 °C) sensitive electron multiplied CCD camera and the prism-type total internal reflection mechanism. A laser combiner was introduced to facilitate simultaneous dual-channel imaging. It has been applied to study the structure, stoichiometry, distance and function of the phi29 DNA packaging motor. Single molecule photobleaching analysis clarified the stoichiometry of pRNA on the motor and elucidated the mechanism of pRNA hexamer assembly. The feasibility of the single-molecule imaging system was demonstrated in single-molecule FRET studies. Distance rulers made of dual-labeled dsDNA and RNA/DNA hybrids were used to evaluate the system. The single-molecule FRET was also applied to the reconstructed the 3D structure of phi29 motor pRNA monomers and pRNA dimers. Ten pRNA monomers labeled with single donor or acceptor fluorophore at various locations were constructed, and eight partner pairs were assembled into dimers. FRET signals were detected and utilized to assess the distance between each donor/acceptor pair. The results provide the distance constraints for computer modeling of the motor. We have also re-engineered the energy conversion protein, gp16, of phi29 motor for single fluorophore labeling to facilitate the single molecule studies of motor mechanism. The potential applications of nanometer localization approaches (SHRImP and SHREC) to the study of the phi29 nanomotor were also investigated.

Reactivity of Human Holocarboxylase Synthetase Toward Biotin-Accepting Substrates

Human Holocarboxylase Synthetase (HCS) catalyzes biotin transfer to carboxylases in a two-step reaction in which the activated biotin, bio-5′-AMP, is first formed from substrates biotin and ATP. The biotin is then transferred to a single lysine residue on the carboxylase. The five substrates for HCS, including acetyl-CoA carboxylases 1 and 2, pyruvate carboxylase, 3-methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, play critical roles in metabolism. Two isoforms of HCS differ at the amino-terminus by 57 amino acids, and their specificity towards the substrates is unknown. The biochemistry of HCS function has been investigated by characterizing the basic properties of the two isoforms and their interactions with the five acceptor-protein substrates. Equilibrium sedimentation indicates that the proteins are monomers in their apo-forms and when bound to the adenylated intermediate. Steady state analysis of the overall reaction indicates that both isoforms possess similar behavior with respect to the small molecule substrates. In contrast, stopped flow fluorescence measurements of biotin transfer indicate that the HCS forms can exhibit distinct association rates with a single biotin acceptor. Moreover, the isoforms display preferential reactivity among the substrates. These results are consistent with a role for HCS N-terminus in acceptor substrate recognition, and suggest a role for HCS in dictating a hierarchy of biotin utilization by carboxylases.

Binding of Small-Molecule Inhibitors To MAP Kinase ERK2, Studied with Resonance Energy Transfer (RET)

The extracellular-signal-regulated kinase (ERK) proteins belong to the mitogen-activated protein kinase family. They participate in several important cell-signaling pathways. Unregulated, ERK2 is thought to mediate cell proliferation in many types of cancer. But because ERK also functions in many normal cell activities, inhibition selectivity is necessary for its use in cancer therapy: one needs to block only phosphorylation of those substrates that are involved in cell proliferation, while leaving phosphorylation of other substrates unaffected. Novel small-molecule compounds, which inhibit phosphorylation of selected substrates but do not compete with ATP for its binding site, have been previously identified by computer-aided drug design (CADD) and molecular-dynamics docking algorithms. Herein, we spectroscopically characterized selected compounds, and show that they can serve as resonance energy transfer (RET) acceptors for tryptophan: we determined the values of spectral overlap J between the compounds' absorption and ERK fluorescence, and of the Forster distance R0 for the compound/tryptophan pairs. We then used RET to determine average distances between the bound compounds and the group of three tryptophans in ERK2, thus validating the CADD predictions of the compounds' binding sites. The problem of multiple but closely located donors (tryptophans) that pass the energy to the single acceptor (the bound compound) is discussed, as is the possibility of utilizing RET for mapping the inhibitor-binding sites on other kinases. The novel RET acceptors for tryptophan can conceivably be employed in studies of other protein/ligand systems with suitable spectroscopic properties.

Anomalous Surplus Energy Transfer Observed with Multiple FRET Acceptors

BackgroundFörster resonance energy transfer (FRET) is a mechanism where energy is transferred from an excited donor fluorophore to adjacent chromophores via non-radiative dipole-dipole interactions. FRET theory primarily considers the interactions of a single donor-acceptor pair. Unfortunately, it is rarely known if only a single acceptor is present in a molecular complex. Thus, the use of FRET as a tool for measuring protein-protein interactions inside living cells requires an understanding of how FRET changes with multiple acceptors. When multiple FRET acceptors are present it is assumed that a quantum of energy is either released from the donor, or transferred in toto to only one of the acceptors present. The rate of energy transfer between the donor and a specific acceptor (kD→A) can be measured in the absence of other acceptors, and these individual FRET transfer rates can be used to predict the ensemble FRET efficiency using a simple kinetic model where the sum of all FRET transfer rates is divided by the sum of all radiative and non-radiative transfer rates.Methodology/Principal FindingsThe generality of this approach was tested by measuring the ensemble FRET efficiency in two constructs, each containing a single fluorescent-protein donor (Cerulean) and either two or three FRET acceptors (Venus). FRET transfer rates between individual donor-acceptor pairs within these constructs were calculated from FRET efficiencies measured after systematically introducing point mutations to eliminate all other acceptors. We find that the amount of energy transfer observed in constructs having multiple acceptors is significantly greater than the FRET efficiency predicted from the sum of the individual donor to acceptor transfer rates.Conclusions/SignificanceWe conclude that either an additional energy transfer pathway exists when multiple acceptors are present, or that a theoretical assumption on which the kinetic model prediction is based is incorrect.

Phenazine–naphthalene-1,5-diamine–water (1/1/2)

The asymmetric unit of the title compound, C12H8N2·C10H10N2·2H2O, contains one half-mol­ecule of phenazine, one half-mol­ecule of naphthalene-1,5-diamine and one water mol­ecule. The phenazine and naphthalene-1,5-diamine mol­ecules are located on inversion centers. The water mol­ecules serve as bridges between the naphthalene-1,5-diamine mol­ecules and also between the naphthalene-1,5-diamine and phenazine mol­ecules. The naphthalene-1,5-diamine and water mol­ecules are connected via N—H⋯O and O—H⋯N hydrogen bonds, forming a T4(2) motif. They are arranged into a two-dimensional polymeric structure parallel to (10) in which the water mol­ecule is a single donor and a double acceptor, whereas the amino group is a double donor and a single acceptor in the hydrogen bonding. These two-dimensional assemblies alternate with the layers of phenazine mol­ecules arranged into a herringbone motif. Each phenazine mol­ecule is hydrogen bonded to two water mol­ecules and thus a three-dimensional framework of hydrogen-bonded mol­ecules is generated.

Possibility of Transport Through a Single Acceptor in a Gate-All-Around Silicon Nanowire PMOSFET

Temperature-dependent electrical transport measurements of cylindrical shaped gate-all-around silicon nanowire p-channel MOSFET were performed. At 4.2 K, they show current oscillations, which can be analyzed by single hole tunneling originated from nanowire quantum dots. In addition to this single hole tunneling, one device exhibited strong current peaks, surviving even at room temperature. The separations between these current peaks corresponded to the energy of 25 and 26 meV. These values were consistent with the sum of the bound-state energy spacing and the charging energy of a single boron atom. The radius calculated from the obtained single-atom charging energy was also comparable to the light-hole Bohr radius.

5-Amino-1-naphthol

In the title compound, C10H9NO, the amino and the hydr­oxy groups act both as a single donor and a single acceptor in hydrogen bonding. In the crystal, mol­ecules are connected via chains of inter­molecular ⋯N—H⋯O—H⋯ inter­actions, forming a two-dimensional polymeric structure resembling the hydrogen-bonded mol­ecular assembly found in the crystal structure of naphthalene-1,5-diol. Within this layer, mol­ecules related by a translation along the a axis are arranged into slipped stacks via π–π stacking inter­actions [inter­planar distance = 3.450 (4) Å]. The amino N atom shows sp 3 hybridization and the two attached H atoms are located on the same side of the aromatic ring.

DEER Distance Measurement Between a Spin Label and a Native FAD Semiquinone in Electron Transfer Flavoprotein

The human mitochondrial electron transfer flavoprotein (ETF) accepts electrons from at least 10 different flavoprotein dehydrogenases and transfers electrons to a single electron acceptor in the inner membrane. Paracoccus denitrificans ETF has the identical function, shares the same three-dimensional structure and functional domains, and exhibits the same conformational mobility. It has been proposed that the mobility of the alphaII domain permits the promiscuous behavior of ETF with respect to a variety of redox partners. Double electron-electron resonance (DEER) measurements between a spin label and an enzymatically reduced flavin adenine dinucleotide (FAD) cofactor in P. denitrificans ETF gave two distributions of distances: a major component centered at 4.2 +/- 0.1 nm and a minor component centered at 5.1 +/- 0.2 nm. Both components had widths of approximately 0.3 nm. A distance of 4.1 nm was calculated using the crystal structure of P. denitrificans ETF, which agrees with the major component obtained from the DEER measurement. The observation of a second distribution suggests that ETF, in the absence of substrate, adopts some conformations that are intermediate between the predominant free and substrate-bound states.

Energetic disorder limits energy transfer in semiconductor nanocrystal–DNA–dye conjugates

We demonstrate the influence of spectral linewidths of individual donor-acceptor couples on energy transfer efficiency in semiconductor nanocrystal–DNA–organic dye conjugates. Temperature-dependent single molecule and ensemble spectroscopy data are analyzed using the Förster theory within the macroscopic and microscopic approaches. The results obtained evidence on the importance of the spectral overlap between emission of a single donor and absorption of a single acceptor in its close vicinity, which determines the microscopic resonance and transfer efficiency between individual neighbors. This realization poses important implications on the applicability of ensemble spectral overlap for the analysis of distance dependencies of nanoscopic objects.

Polaronic hole localization and multiple hole binding of acceptors in oxide wide-gap semiconductors

Acceptor-bound holes in oxides often localize asymmetrically at one out of several equivalent oxygen ligands. Whereas Hartree-Fock (HF) theory overly favors such symmetry-broken polaronic hole localization in oxides, standard local-density (LD) calculations suffer from spurious delocalization among several oxygen sites. These opposite biases originate from the opposite curvatures of the energy as a function of the fractional occupation number $n$, i.e., ${d}^{2}E/d{n}^{2}<0$ in HF and ${d}^{2}E/d{n}^{2}>0$ in LD. We recover the correct linear behavior, ${d}^{2}E/d{n}^{2}=0$, that removes the (de)localization bias by formulating a generalized Koopmans condition. The correct description of oxygen hole localization reveals that the cation-site nominal single acceptors in ZnO, ${\text{In}}_{2}{\text{O}}_{3}$, and ${\text{SnO}}_{2}$ can bind multiple holes.