Description of the Adsorption and Exciton Delocalizing Properties of p-Substituted Thiophenols on CdSe Quantum Dots.

This work describes the quantitative characterization of the interfacial chemical and electronic structure of CdSe quantum dots (QDs) coated in one of five p-substituted thiophenolates (X-TP, X = NH2, CH3O, CH3, Cl, or NO2), and the dependence of this structure on the p-substituent X. (1)H NMR spectra of mixtures of CdSe QDs and X-TPs yield the number of X-TPs bound to the surface of each QD. The binding data, in combination with the shift in the energy of the first excitonic peak of the QDs as a function of the surface coverage of X-TP and Raman and NMR analysis of the mixtures, indicate that X-TP binds to CdSe QDs in at least three modes, two modes that are responsible for exciton delocalization and a third mode that does not affect the excitonic energy. The first two modes involve displacement of OPA from the QD core, whereas the third mode forms cadmium-thiophenolate complexes that are not electronically coupled to the QD core. Fits to the data using the dual-mode binding model also yield the values of Δr1, the average radius of exciton delocalization due to binding of the X-TP in modes 1 and 2. A 3D parametrized particle-in-a-sphere model enables the conversion of the measured value of Δr1 for each X-TP to the height of the potential barrier that the ligand presents for tunneling of excitonic hole into the interfacial region. The height of this barrier increases from 0.3 to 0.9 eV as the substituent, X, becomes more electron-withdrawing.

Role of Interligand Coupling in Determining the Interfacial Electronic Structure of Colloidal CdS Quantum Dots.

Displacement of cadmium oleate (Cd(oleate)2) ligands for the exciton-delocalizing ligand 4-hexylphenyldithiocarbamate (C6-PTC) on the surfaces of CdS quantum dots (QDs) causes a decrease in the band gap (Eg) of the QD of ∼100 meV for QDs with a radius of 1.9 nm and ∼50 meV for QDs with a radius of 2.5 nm. The primary mechanism of this decrease in band gap, deduced in previous work, is a decrease in the confinement barrier for the excitonic hole. The increase in apparent excitonic radius of the QD that corresponds to this decrease in Eg is denoted ΔR. The dependence of ΔR on the surface coverage of C6-PTC, measured by (1)H NMR spectroscopy, appears to be nonlinear. Calculations of the excitonic energy of a CdS QD upon displacement of native insulating ligands with exciton-delocalizing ligands using a 3D spherical potential well model show that this response includes the contributions to ΔR from both isolated, bound C6-PTC ligands and groups of adjacent C6-PTC ligands. Fits to the experimental plots of ΔR vs surface coverage of C6-PTC with a statistical model that includes the probability of formation of clusters of bound C6-PTC on the QD surface allow for the extraction of the height of the confinement barrier presented by a single, isolated C6-PTC molecule to the excitonic hole. This barrier height is less than 0.6 eV for QDs with a radius of 1.9 nm and between 0.6 and 1.2 eV for QDs with a radius of 2.5 nm.

Enhanced rate of radiative decay in CdSe quantum dots upon adsorption of an exciton-delocalizing ligand.

This paper describes the enhancement of the quantum yield of photoluminescence (PL) of CdSe quantum dots (QDs) upon the adsorption of an exciton-delocalizing ligand, phenyldithiocarbamate. Increasing the apparent excitonic radius by only 10% increases the value of the radiative rate constant by a factor of 1.8 and the PL quantum yield by a factor of 2.4. Ligand exchange therefore simultaneously perturbs the confinement energy of charge carriers and enhances the probability of band-edge transitions.

Control of exciton confinement in quantum dot-organic complexes through energetic alignment of interfacial orbitals.

This paper describes a method to control the quantum confinement, and therefore the energy, of excitonic holes in CdSe QDs through adsorption of the hole-delocalizing ligand phenyldithiocarbamate, PTC, and para substitutions of the phenyl ring of this ligand with electron-donating or -withdrawing groups. These substitutions control hole delocalization in the QDs through the energetic alignment of the highest occupied orbitals of PTC with the highest density-of-states region of the CdSe valence band, to which PTC couples selectively.

Optical Properties of Strongly Coupled Quantum Dot-Ligand Systems.

This Perspective describes the mechanisms by which organic surfactants, in particular, phenyldithiocarbamates (PTCs), couple electronically to the delocalized states of semiconductor quantum dots (QDs). This coupling reduces the confinement energies of excitonic carriers and, in the case of PTC, the optical band gap of metal chalcogenide QDs by up to 1 eV by selectively delocalizing the excitonic hole. The reduction of confinement energy for the hole is enabled by the creation of interfacial electronic states near the valence band edge of the QD. The PTC case illuminates the general minimal requirements for surfactants to achieve observable bathochromic or hypsochromic shifts of the optical band gap of QDs; these include frontier orbitals with energies near the relevant semiconductor band edge, the correct symmetry to mix with the orbitals of the relevant band, and an adsorption geometry that permits spatial overlap between the orbitals of the ligand and those of the relevant band (Se 4p orbitals for CdSe, for example). The shift is enhanced by energetic resonance of frontier orbitals of the surfactant with a high density of states region of the band, which, for CdSe, is ∼1 eV below the band edge. The Perspective discusses other examples of strong-coupling surfactants and compares the orbital mixing mechanism with other mechanisms of surfactant-induced shifts in the QD band gap.

High-contrast photopatterning of photoluminescence within quantum dot films through degradation of a charge-transfer quencher.

Diffraction-limited, high-contrast photopatterning of the photoluminescence of layer-by-layer films comprising CdSe@CdS@ZnS quantum dots and polyviologen is reported. The photoluminescence of the quantum dots is initially quantitatively quenched due to ultrafast photoinduced electron transfer to polyviologen. Photopatterning is achieved by high-power or prolonged illumination in air, which photochemically degrades the polyviologen and thereby restores the photoluminescence of the quantum dots.

Model for adsorption of ligands to colloidal quantum dots with concentration-dependent surface structure.

A study of the adsorption equilibrium of solution-phase CdS quantum dots (QDs) and acid-derivatized viologen ligands (N-[1-heptyl],N'-[3-carboxypropyl]-4,4'-bipyridinium dihexafluorophosphate, V(2+)) reveals that the structure of the surfaces of the QDs depends on their concentration. This adsorption equilibrium is monitored through quenching of the photoluminescence of the QDs by V(2+) upon photoinduced electron transfer. When modeled with a simple Langmuir isotherm, the equilibrium constant for QD-V(2+) adsorption, K(a), increases from 6.7 × 10(5) to 8.6 × 10(6) M(-1) upon decreasing the absolute concentration of the QDs from 1.4 × 10(-6) to 5.1 × 10(-8) M. The apparent increase in K(a) upon dilution results from an increase in the mean number of available adsorption sites per QD from 1.1 (for [QD] = 1.4 × 10(-6) M) to 37 (for [QD] = 5.1 × 10(-8) M) through desorption of native ligands from the surfaces of the QDs and through disaggregation of soluble QD clusters. A new model based on the Langmuir isotherm that treats both the number of adsorbed ligands per QD and the number of available binding sites per QD as binomially distributed quantities is described. This model yields a concentration-independent value for K(a) of 8.7 × 10(5) M(-1) for the QD-V(2+) system and provides a convenient means for quantitative analysis of QD-ligand adsorption in the presence of competing surface processes.

A molecule to detect and perturb the confinement of charge carriers in quantum dots.

This paper describes unprecedented bathochromic shifts (up to 970 meV) of the optical band gaps of CdS, CdSe, and PbS quantum dots (QDs) upon adsorption of an organic ligand, phenyldithiocarbamate (PTC), and the use of PTC to map the quantum confinement of specific charge carriers within the QDs as a function of their radius. For a given QD material and physical radius, R, the magnitude of the increase in apparent excitonic radius (ΔR) upon delocalization by PTC directly reflects the degree of quantum confinement of one or both charge carriers. The plots of ΔR vs R for CdSe and CdS show that exciton delocalization by PTC occurs specifically through the excitonic hole. Furthermore, the plot for CdSe, which spans a range of R over multiple confinement regimes for the hole, identifies the radius (R∼1.9 nm) at which the hole transitions between regimes of strong and intermediate confinement. This demonstration of ligand-induced delocalization of a specific charge carrier is a first step toward eliminating current-limiting resistive interfaces at organic-inorganic junctions within solid-state hybrid devices. Facilitating carrier-specific electronic coupling across heterogeneous interfaces is especially important for nanostructured devices, which comprise a high density of such interfaces.

RNA-seq: technical variability and sampling.

BACKGROUND: RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript. RESULTS: In this study three independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage. CONCLUSIONS: Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases.