Mechanistic study of the atomic layer deposition of cobalt: a combined mass spectrometric and computational approach.

Cobaltcarbonyl-tert-butylacetylene (CCTBA) is a conventional precursor for the selective atomic layer deposition of Co onto silicon surfaces. However, a limited understanding of the deposition mechanism of such cobalt precursors curbs rational improvements on their design for increased efficiency and tuneable selectivity. The impact of using a less reactive internal alkyne instead of a terminal alkyne was investigated using experimental and computational methods. Using electrospray-ionization mass spectrometry, the formation of CCTBA analogs and their gas phase decomposition pathways were studied. Decomposition experiments show very similar decomposition pathways between the two complexes. The internal alkyne dissociates from the Co complex at slightly lower energies than the terminal alkyne, suggesting that an internal alkynyl ligand may be more suited to low temperature ALD. In addition, transition state calculations using the nudged elastic band method confirm an increased reaction barrier between the internal alkyne and the Si-H surface bonds on Si(111). These results suggests that using a less reactive internal alkyne will result in fewer embedded carbon impurities during deposition onto Si wafers. DFT calculations using the PBE functional and periodic boundary conditions also predict increased surface binding with the metal centers of the internal alkynyl complex.

Coupling Perovskite Quantum Dot Pairs in Solution using a Nanoplasmonic Assembly.

Perovskite quantum dots (PQDs) provide a robust solution-based approach to efficient solar cells, bright light emitting devices, and quantum sources of light. Quantifying heterogeneity and understanding coupling between dots is critical for these applications. We use double-nanohole optical trapping to size individual dots and correlate to emission energy shifts from quantum confinement. We were able to assemble a second dot in the trap, which allows us to observe the coupling between dots. We observe a systematic red-shift of 1.1 ± 0.6 meV in the emission wavelength. Theoretical analysis shows that the observed shift is consistent with resonant energy transfer and is unusually large due to moderate-to-large quantum confinement in PQDs. This demonstrates the promise of PQDs for entanglement in quantum information applications. This work enables future in situ control of PQD growth as well as studies of the coupling between small PQD assemblies with quantum information applications in mind.

Trichloro(Dinitrogen)Platinate(II).

Zeise's salt, [PtCl3 (H2 C=CH2 )]- , is the oldest known organometallic complex, featuring ethylene strongly bound to a platinum salt. Many derivatives are known, but none involving dinitrogen, and indeed dinitrogen complexes are unknown for both platinum and palladium. Electrospray ionization mass spectrometry of K2 [PtCl4 ] solutions generate strong ions corresponding to [PtCl3 (N2 )]- , the identity of which was confirmed through ion-mobility spectrometry and MS/MS experiments that proved it to be distinct from its isobaric counterparts [PtCl3 (C2 H4 )]- and [PtCl3 (CO)]- . Computational analysis established a gas-phase platinum-dinitrogen bond strength of 116 kJ mol-1 , substantially weaker than the ethylene and carbon monoxide analogues but stronger than for polar solvents such as water, methanol and dimethylformamide, and strong enough that the calculated N-N bond length of 1.119 Šrepresents weakening to a degree typical of isolated dinitrogen complexes.

Pan-specific and partially selective dye-labeled peptidic inhibitors of the polycomb paralog proteins.

Epigenetic regulation of gene expression is in part controlled by post-translational modifications on histone proteins. Histone methylation is a key epigenetic mark that controls gene transcription and repression. There are five human polycomb paralog proteins (Cbx2/4/6/7/8) that use their chromodomains to recognize trimethylated lysine 27 on histone 3 (H3K27me3). Recognition of the methyllysine side chain is achieved through multiple cation-pi interactions within an 'aromatic cage' motif. Despite high structural similarity within the chromodomains of this protein family, they each have unique functional roles and are linked to different cancers. Selective inhibition of different CBX proteins is desirable for both fundamental studies and potential therapeutic applications. We report here on a series of peptidic inhibitors that target certain polycomb paralogs. We have identified peptidic scaffolds with sub-micromolar potency, and will report examples that are pan-specific and that are partially selective for individual members within the family. These results highlight important structure-activity relationships that allow for differential binding to be achieved through interactions outside of the methyllysine-binding aromatic cage motif.

Accelerated Structural Prediction of Flexible Protein-Ligand Complexes: The SLICE Method.

Using existing and academically available software, we present a new method for the structural prediction of binding events containing flexible protein targets. SLICE (Selective Ligand-Induced Conformational Ensemble) combines opportunistic stochastic jumps of ligand position with standard molecular dynamics to model the induced-fit binding of ligands starting with unbound host coordinates. To induce the structural adaptations of the complex at the binding site, conformational jumps in ligand position are selected in SLICE from structures generated by a docking software. Multiple binding trajectories from the docking set are followed using molecular dynamics for a set time to relax the host structure and generate new host poses. A new configurational jump is made on the set of newly generated host poses. The process is then repeated. The method was implemented with AutoDock Vina as the docking method, Vina scores as the selection criterion, and Amber code for molecular dynamics and applied to several test systems. A system consisting of Chromobox protein homologue 8 (CBX8) and its small peptide ligand, H3K9Me3, for which the final (bound) configuration is known, is used for verifying SLICE in the present setup. The setup was also applied to several nonpeptide molecules on known difficult flexible targets exhibiting a large disparity between apo and holo host states. The SLICE simulations provide a promising approach to generate induced-fit configurations compared to existing long (microsecond) classical and accelerated dynamics approaches in all the test systems considered here. However, further optimization of SLICE parameters is required for replicating crystal structure coordinates for some systems. We discuss in the following pages the various SLICE parameters and how they can be optimized for the system at hand.

Structural analysis of helicene molecules adsorbed on symmetric surfaces.

Helicenes are chiral polyaromatic hydrocarbon molecules which self-assemble into ordered monolayers on solid substrates, and are of current interest in the study of supramolecular systems and the development of smart materials. In this work we investigate the geometry of helicene monomers and stacked dimers on (111) facets of coinage metals. The geometry of the adsorbed molecules is shaped by the coupling of intermolecular dispersive forces, intramolecular steric repulsion between end rings and surface-molecule interactions. Thus, binding and stereospecificity outcomes vary broadly depending on the identity of molecule/surface pair. Overall, homochiral interactions are found to be more effective than heterochiral stacking, due to a better fit between the helical structures in like dimers. On a surface, this effect is enhanced by the flattening of surface-proximal molecular rings. However, our results show that the "sandwich" effect of the second molecular layer increases molecular footprints in the first layer, with potentially large implications in monolayer organization and surface commensuration.

Fundamental aspects in surface self-assembly: theoretical implications of molecular polarity and shape.

We investigate fundamental aspects of structure formation in molecular self-assembly, by examining the emergence of order upon adsorption of a series of model molecules. It is known that strongly polar diatomic molecules form three-dimensional crystals in the absence of a substrate. This tendency can be disrupted upon assembly on a solid surface, and various other types of order may arise. Depending on the relative strength of the interactions, disordered phases, two-dimensional crystals commensurate to the surface, and unmodified crystals were observed upon adsorption of simple dipoles in the present work. Introduction of steric features, in the form of a longer backbone or substituents external to the polar pair, led to even richer phase diagrams. The formation of two-dimensional phases with nematic (parallel) or antiparallel alignment was accomplished by altering the polarity of the end groups on needle-like molecules, whereas embedded charged groups made two-dimensional structure unstable for even very long molecules. These molecules preferred to align in long, often desorbed, molecular wires. The wealth of phases observed here parallel the results of experimental systematic or incidental studies of the relationships between molecular interactions and self-assembled patterns, and provide some insight into the molecular handles that self-assembly researchers can wield to guide the process towards a desired structural outcome.

A reactivity model for oxidative addition to palladium enables quantitative predictions for catalytic cross-coupling reactions.

Making accurate, quantitative predictions of chemical reactivity based on molecular structure is an unsolved problem in chemical synthesis, particularly for complex molecules. We report an approach to reactivity prediction for catalytic reactions based on quantitative structure-reactivity models for a key step common to many catalytic mechanisms. We demonstrate this approach with a mechanistically based model for the oxidative addition of (hetero)aryl electrophiles to palladium(0), which is a key step in myriad catalytic processes. This model links simple molecular descriptors to relative rates of oxidative addition for 79 substrates, including chloride, bromide and triflate leaving groups. Because oxidative addition often controls the rate and/or selectivity of palladium-catalyzed reactions, this model can be used to make quantitative predictions about catalytic reaction outcomes. Demonstrated applications include a multivariate linear model for the initial rate of Sonogashira coupling reactions, and successful site-selectivity predictions for Suzuki, Buchwald-Hartwig, and Stille reactions of multihalogenated substrates relevant to the synthesis of pharmaceuticals and natural products.

Tuning the dielectric response in a nanocomposite material through nanoparticle morphology.

Ceramic materials such as metal oxides, mixed metal oxides and silicates, constitute a broadly-used, high-performance technology for electronic insulators. The introduction of metal cluster dopants and molecular-scale inclusions in a dielectric matrix provides an opportunity for manufacturing new high-κ solid-state dielectrics with tunable field-response properties. The quantum properties of these metallic nanoparticles depend strongly on their size and shape, a characteristic that can be exploited in changing the response properties of a material, whereas the small nanoparticle size can help limit the issues of conduction and current leakage. Here, we model the polarization of molecular-scale silver inclusions in a magnesium oxide matrix, using the Modern Theory of Polarization and Car-Parrinello Molecular Dynamics (CPMD). Details of the implementation are laid out, including handling of current jumps due to the distortion of the matrix during the simulation. Several trends in the dielectric response are considered in this work, including the effects of nanoparticle size, shape and orientation relative to the applied field. Dielectric permittivity enhancements of 30-100% are observed with inclusion sizes varying from 8 to 32 atoms, considering both rod-like and disk-like inclusions, with alignment either parallel or perpendicular to the external field.

A broadly applicable quantitative relative reactivity model for nucleophilic aromatic substitution (SNAr) using simple descriptors.

We report a multivariate linear regression model able to make accurate predictions for the relative rate and regioselectivity of nucleophilic aromatic substitution (SNAr) reactions based on the electrophile structure. This model uses a diverse training/test set from experimentally-determined relative SNAr rates between benzyl alcohol and 74 unique electrophiles, including heterocycles with multiple substitution patterns. There is a robust linear relationship between the experimental SNAr free energies of activation and three molecular descriptors that can be obtained computationally: the electron affinity (EA) of the electrophile; the average molecular electrostatic potential (ESP) at the carbon undergoing substitution; and the sum of average ESP values for the ortho and para atoms relative to the reactive center. Despite using only simple descriptors calculated from ground state wavefunctions, this model demonstrates excellent correlation with previously measured SNAr reaction rates, and is able to accurately predict site selectivity for multihalogenated substrates: 91% prediction accuracy across 82 individual examples. The excellent agreement between predicted and experimental outcomes makes this easy-to-implement reactivity model a potentially powerful tool for synthetic planning.

Toward designed singlet fission: electronic states and photophysics of 1,3-diphenylisobenzofuran.

Single crystal molecular structure and solution photophysical properties are reported for 1,3-diphenylisobenzofuran (1), of interest as a model compound in studies of singlet fission. For the ground state of 1 and of its radical cation (1(+*)) and anion (1(-*)), we report the UV-visible absorption spectra, and for neutral 1, also the magnetic circular dichroism (MCD) and the decomposition of the absorption spectrum into purely polarized components, deduced from fluorescence polarization. These results were used to identify a series of singlet excited states. For the first excited singlet and triplet states of 1, the transient visible absorption spectra, S(1) --> S(x) and sensitized T(1) --> T(x), and single exponential lifetimes, tau(F) = approximately 5.3 ns and tau(T) = approximately 200 micros, are reported. The spectra and lifetimes of S(1) --> S(0) fluorescence and sensitized T(1) --> T(x) absorption of 1 were obtained in a series of solvents, as was the fluorescence quantum yield, Phi(F) = 0.95-0.99. No phosphorescence has been detected. The first triplet excitation energy of solid 1 (11,400 cm(-1)) was obtained by electron energy loss spectroscopy, in agreement with previously reported solution values. The fluorescence excitation spectrum suggests an onset of a nonradiative channel at approximately 37,000 cm(-1). Excitation energies and relative transition intensities are in agreement with those of ab initio (CC2) calculations after an empirical 3000 cm(-1) adjustment of the initial state energy to correct differentially for a better quality description of the initial relative to the terminal state of an absorption transition. The interpretation of the MCD spectrum used the semiempirical PPP method, whose results for the S(0) --> S(x) spectrum require no empirical adjustment and are otherwise nearly identical with the CC2 results in all respects including the detailed nature of the electronic excitation. The ground state geometry of 1 was also calculated by the MP2, B3LYP, and CAS methods. The calculations provided a prediction of changes of molecular geometry upon excitation or ionization and permitted an interpretation of the spectra in terms of molecular orbitals involved. Computations suggest that 1 can exist as two nearly isoenergetic conformers of C(2) or C(s) symmetry. Linear dichroism measurements in stretched polyethylene provide evidence for their existence and show that they orient to different degrees, permitting a separation of their spectra in the region of the purely polarized first absorption band. Their excitation energies are nearly identical, but the Franck-Condon envelopes of their first transition differ to a surprising degree.

Reactive metallocene cations as sensitive indicators of gas-phase oxygen and water.

Analysis of highly reactive compounds at very low concentration in solution using electrospray ionization mass spectrometry requires the use of exhaustively purified solvents. It has generally been assumed that desolvation gas purity needs to be similarly high, and so most chemists working in this space have relied upon high purity gas. However, the increasing competitiveness of nitrogen generators, which provide gas purity levels that vary inversely with flow rate, prompted an investigation of the effect of gas-phase oxygen on the speciation of ions. The most reactive species studied, the reduced titanium complex [Cp2Ti(NCMe)2]+[ZnCl3]- and the olefin polymerization pre-catalyst [Cp2Zr(µ-Me)2AlMe2]+[B(C6F5)4]-, only exhibited detectable oxidation when they were rendered coordinatively unsaturated through in-source fragmentation. Computational chemistry allowed us to find the most plausible pathways for the observed chemistry in the absence of observed intermediates. The results provide insight into the gas-phase oxidation or hydrolysis of these reactive species.

PANX1 in inflammation heats up: New mechanistic insights with implications for injury and infection.

A new study by Yang and colleagues has revealed that TNF-alpha regulates PANX1 levels through an NF-kB-dependent mechanism in human endothelial cells. PANX1 modulates Ca2+ influx contributing to IL-1beta production independent of purinergic signaling. These novel findings expand our understanding of TNF-alpha-mediated upregulation of IL-1beta with implications for responses to tissue injury and infection.

Optimization of Ligands Using Focused DNA-Encoded Libraries To Develop a Selective, Cell-Permeable CBX8 Chromodomain Inhibitor.

Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2, CBX4, CBX6, CBX7, and CBX8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarities in sequence and structure among the CBX ChDs provide a major obstacle in developing selective CBX ChD inhibitors. Here we report the selection of small, focused, DNA-encoded libraries (DELs) against multiple homologous ChDs to identify modifications to a parental ligand that confer both selectivity and potency for the ChD of CBX8. This on-DNA, medicinal chemistry approach enabled the development of SW2_110A, a selective, cell-permeable inhibitor of the CBX8 ChD. SW2_110A binds CBX8 ChD with a Kd of 800 nM, with minimal 5-fold selectivity for CBX8 ChD over all other CBX paralogs in vitro. SW2_110A specifically inhibits the association of CBX8 with chromatin in cells and inhibits the proliferation of THP1 leukemia cells driven by the MLL-AF9 translocation. In THP1 cells, SW2_110A treatment results in a significant decrease in the expression of MLL-AF9 target genes, including HOXA9, validating the previously established role for CBX8 in MLL-AF9 transcriptional activation, and defining the ChD as necessary for this function. The success of SW2_110A provides great promise for the development of highly selective and cell-permeable probes for the full CBX family. In addition, the approach taken provides a proof-of-principle demonstration of how DELs can be used iteratively for optimization of both ligand potency and selectivity.

High-speed imaging of surface-enhanced Raman scattering fluctuations from individual nanoparticles.

The concept of plasmonic hotspots is central to the interpretation of the surface-enhanced Raman scattering (SERS) effect. Although plasmonic hotspots are generally portrayed as static features, single-molecule SERS (SM-SERS) is marked by characteristic time-dependent fluctuations in signal intensity. The origin of those fluctuations can be assigned to a variety of dynamic and complex processes, including molecular adsorption or desorption, surface diffusion, molecular reorientation and metal surface reconstruction. Since each of these mechanisms simultaneously contributes to a fluctuating SERS signal, probing their relative impact in SM-SERS remains an experimental challenge. Here, we introduce a super-resolution imaging technique with an acquisition rate of 800,000 frames per second to probe the spatial and temporal features of the SM-SERS fluctuations from single silver nanoshells. The technique has a spatial resolution of ~7 nm. The images reveal short ~10 µs scattering events localized in various regions on a single nanoparticle. Remarkably, even a fully functionalized nanoparticle was 'dark' more than 98% of the time. The sporadic SERS emission suggests a transient hotspot formation mechanism driven by a random reconstruction of the metallic surface, an effect that dominates over any plasmonic resonance of the particle itself. Our results provide the SERS community with a high-speed experimental approach to study the fast dynamic properties of SM-SERS hotspots in typical room-temperature experimental conditions, with possible implications in catalysis and sensing.

Low-frequency polarization in molecular-scale noble-metal/metal-oxide nanocomposites.

Materials with high dielectric permittivity are highly desirable in the electronics industry. One avenue for enhancing the permittivity of standard metal oxide and ceramic dielectrics is to incorporate nanoscale Ag and Au inclusions in the material. Given the small scale of modern day devices, these inclusions will necessarily be up to a few nanometers in size. We develop methodology by which polarization in nanocomposites with molecular-scale inclusions can be obtained from first-principles calculations, and partitioned into inclusion and matrix contributions. The methodology is applied to a model Ag8/MgO nanocomposite. A 4% volume loading of Ag8 nanoparticles leads to a 30% enhancement of the dielectric permittivity. The enhancement arises from both the electronic polarization of the nanoparticle and the additional polarization of matrix ions in the interfacial region.

High-capacitance organic nanodielectrics: effective medium models of their response.

Molecular and macromolecular high-permittivity organic gate dielectric materials have been the focus of recent experimental research as a consequence of their promising properties for organic and inorganic field effect transistor (FET) applications. Two types of molecular thin films, self-assembled nanodielectrics (SANDs) and cross-linked polymer blends (CPBs), have been shown experimentally to afford high capacitances and low FET operating voltages. In an effort to design optimized nanostructures having even larger capacitances, lower leakage current densities, and further reduced FET operating voltages, we discuss approaches for computing the effective permittivities of each nanodielectric motif and investigate how molecular arrangements impact overall device capacitance. The calculated frequency-dependent capacitances, derived from Maxwell-Wagner theory applied to the Maxwell-Garnett effective medium approximation, agree fairly well with the experimental values for the two types of nanodielectrics. Predictions of larger capacitance SANDs are made with the two-capacitors-in-series equivalent circuit, where the layered, self-assembled structure is viewed as two different capacitors. The Maxwell-Garnett and Polder-Van Santen effective medium approximations are used to predict the dielectric response of higher permittivity polymer cross-linked blends. In calculations showing good agreement between theory and experiment, and with all parameters being equal, it is found that greater capacitances should be achievable with cross-linked composites than with layered composites.

Surface-site reactivity in small-molecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters.

BACKGROUND: The adsorption of organic molecules on metal surfaces has a broad array of applications, from device engineering to medical diagnosis. The most extensively investigated class of metal-molecule complexes is the adsorption of thiols on gold. RESULTS: In the present manuscript, we investigate the dependence of methylthiol adsorption structures and energies on the degree of unsaturation at the metal binding site. We designed an Au20 cluster with a broad range of metal site coordination numbers, from 3 to 9, and examined the binding conditions of methylthiol at the various sites. CONCLUSION: We found that despite the small molecular size, the dispersive interactions of the backbone are a determining factor in the molecular affinity for various sites. Kink sites were preferred binding locations due to the availability of multiple surface atoms for dispersive interactions with the methyl groups, whereas tip sites experienced low affinity, despite having low coordination numbers.

Selective Inhibition of CBX6: A Methyllysine Reader Protein in the Polycomb Family.

The polycomb paralogs CBX2, CBX4, CBX6, CBX7, and CBX8 are epigenetic readers that rely on "aromatic cage" motifs to engage their partners' methyllysine side chains. Each CBX carries out distinct functions, yet each includes a highly similar methyllysine-reading chromodomain as a key element. CBX7 is the only chromodomain that has yet been targeted by chemical inhibition. We report a small set of peptidomimetic agents in which a simple chemical modification switches the ligands from one with promiscuity across all polycomb paralogs to one that provides selective inhibition of CBX6. The structural basis for this selectivity, which involves occupancy of a small hydrophobic pocket adjacent to the aromatic cage, was confirmed through molecular dynamics simulations. Our results demonstrate the increases in affinity and selectivity generated by ligands that engage extended regions of chromodomain binding surfaces.

Structural behavior and self-assembly of Lennard-Jones clusters on rigid surfaces.

The phase behavior and surface pattern formation for intermediate size Lennard-Jones clusters on rigid surfaces are examined. We use a parallel tempering Monte Carlo algorithm, in the canonical ensemble. Tempering is done over the temperature domain in most of the calculations. A two-dimensional temperature and Hamiltonian tempering algorithm is also implemented, to examine its usefulness in investigating this type of problem. In general, we observe gas phase systems as they undergo a condensation transition on the surface, followed by a freezing transition. The final solid state pattern formed by the cluster on the surface is the result of a number of competing effects. First, there is a competition between attraction within the cluster and that between cluster and surface atoms. Second, a monolayer of Lennard-Jones atoms tends to pack in a hexadic geometry. This geometry is frustrated on a surface with a different symmetry. The molecular organization of the substrate has a serious impact on the cluster packing. The surface morphology and the size mismatch between cluster and surface atoms, along with the relative interaction strengths, determine which of the effects prevail. When the surface atoms are small enough, the interactions within the cluster determine the symmetry of the pattern. In such a case, the substrate behaves similarly to a continuous surface, and the low-temperature pattern is a hexadic monolayer. When the sizes of the surface and cluster atoms are comparable, the low-temperature adsorbed geometry mimics the substrate symmetry. On a face-centered cubic surface, face-centered cubic monolayers or droplets are obtained.