Polymerization of Physisorbed Molecular Monolayers via Overhanging Alkynyl Chains: Characterization of Polymerization Kinetics and Monolayer Durability.

Monolayers self-assembled by triphenyleneethynylene (TPE) compounds bearing two terminal alkynyl chains were polymerized by Glaser-Hay (G-H) alkyne coupling at the acetonitrile-HOPG interface. The alkynyl chains extend into the solution due to the monolayer's dense-packed morphology. Reacting substructures that have no morphology-determining roles is a potential strategy for preserving monolayer morphology throughout polymerization. Monolayer G-H reaction kinetics and polymerized monolayer durability were characterized by using mass spectrometry and fluorescence. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) and time-of-flight (TOF) MS were used to identify TPE-oligomers in the monolayer and to track the monolayer populations of TPE-monomer, -dimer, and -trimer as a function of G-H reaction duration. Comparison of the observed kinetics to a Monte Carlo simulation provided evidence of step-growth polymerization. The durability of polymerized monolayers depended strongly on the length of the alkynyl chains linked by G-H reaction. Polymerized T6y monolayers (O(CH2)3C≡CH alkynyl chains) desorbed minimally during 16-h immersion in 90 °C o-dichlorobenzene (oDCB), whereas polymerized T8y (O(CH2)5C≡CH alkynyl chains) and polymerized T11y (O(CH2)8C≡CH alkynyl chains), desorbed 33 and 60%, respectively, of their TPE units after 4 h in 90 °C oDCB. All the polymerized monolayers are much more durable than unpolymerized monolayers, which desorb quantitatively from HOPG when rinsed with 25 µL of oDCB. Polymerized T6y monolayer is a highly durable anchor that may be adapted to build multilayer structures "permanently" attached to the HOPG surface. The alkynyl chain length dependence may be useful for tuning polymerized TPE monolayer durability for specific applications.

Reactive two-component monolayers template bottom-up assembly of nanoparticle arrays on HOPG.

Two triphenyleneethynylene derivatives, 1OH and 2, self-assemble a patterned monolayer (ML) at the solution-graphite (HOPG) interface. The four molecule unit cell of the ML, (1OH1OH22), spans 19 nm and contains adjacent columns of 1OH molecules spaced by 4.7 nm. Following ML assembly, a disulfide is appended to the alcohol group on each 1OH molecule and used to capture 2.0 nm gold nanoparticles (AuNP). The patterned monolayer directs bottom-up assembly of a 5 nm/19 nm double pitch AuNP pattern.

Zipping and unzipping monolayers: switchable monolayer oligomerization and adhesion via thiol-disulfide interconversion.

Triphenyleneethynylene (TPE) monolayers at the solution-HOPG interface are oligomerized by the oxidation of pendant thioethers to form disulfide cross-links. The oligomerized TPE monolayer adheres strongly to HOPG. Disulfide reduction unzips the oligomers to form a monomeric TPE monolayer with pendant thiols. Subsequent oxidation and reduction treatments zip and unzip the monolayer.

Tracking Invisible Transformations of Physisorbed Monolayers: LDI-TOF and MALDI-TOF Mass Spectrometry as Complements to STM Imaging.

Triphenyleneethynylene (TPEE) derivatives bearing one long aliphatic chain on each terminal aryl ring and two short aliphatic chains on the central aryl ring (core chains) self-assemble single component and 1-D patterned, two-component, crystalline monolayers at the solution-graphite interface. The monolayer morphology directs the core chains off the graphite, making them accessible for chemical reactions but invisible to imaging by scanning tunneling microscopy (STM). This precludes using STM to monitor transformations of the core chains, either by reaction or solution-monolayer exchange of TPEE molecules. Laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) successfully identifies TPEE compounds within physisorbed monolayers. The LDI-TOF spectra of TPEE monolayer-graphite samples exhibit strong molecular ion peaks and minimal fragmentation or background. LDI-TOF and STM techniques are combined to evaluate monolayer composition and morphology, track solution-monolayer exchange, to identify reaction products and to measure kinetics of chemical reactions at the solution-monolayer interface. LDI-TOF MS provides rapid qualitative evaluation of monolayer composition across a graphite substrate. Challenges to quantitative composition evaluation by LDI-TOF include compound-specific light absorption, surface desorption/ionization and fragmentation characteristics. For some, but not all, compounds, applying matrix onto a self-assembled monolayer increases molecular ion intensities and affords more accurate assessment of monolayer composition via matrix assisted laser desorption/ionization (MALDI) MS. Matrix addition precludes subsequent chemical or STM studies of the monolayer, whereas reactions and STM may be performed at nonirradiated regions following LDI-TOF measurements. LDI- and MALDI-TOF MS are useful complements to STM and are easily implemented tools for study of physisorbed monolayers.

Shape-Directed Patterning and Surface Reaction of Tetra-diacetylene Monolayers: Formation of Linear and Two-Dimensional Grid Polydiacetylene Alternating Copolymers.

Side chains containing two diacetylene units spaced by an odd number of methylene units exhibit pronounced "bumps" composed of 0.3 nm steps, in opposite directions, at odd and even side-chain positions. In densely packed self-assembled monolayers, the bis-diacetylene bumps stack into each other, similar to the stacking of paper cups. Bis-diacetylene side chain structure and associated packing constraints can be tailored by altering the bump width, direction, side-chain location, and overall side-chain length as a means to direct the identities and alignments of adjacent molecules within monolayers. Scanning tunneling microscopy (STM) at the solution­HOPG interface confirms the high selectivity and fidelity with which bis-diacetylene bump stacking directs the packing of shape-complementary side chains within one-component monolayers and within two-component, 1-D self-patterned monolayers. Drop cast or moderately annealed monolayers of anthracenes bearing two bis-diacetylene side chains assemble single domains as large as 10(5) nm2. Light-induced cross-linking of two-component, 1-D patterned monolayers generates linear polydiacetylene alternating copolymers (A-B-)x and 2-D grid polydiacetylene alternating copolymers (A(-B-)(-B-)A(-B-)(-B-))x that covalently lock in monolayer structure and patterns.

Shape Amphiphiles in 2-D: Assembly of 1-D Stripes and Control of Their Surface Density.

The morphology of monolayers assembled from mixtures of a shape-amphiphilic molecule, {33,19} = 1-((hentriaconta-14,16-diyn-1-yloxy)methyl)-5-((heptadecyloxy)methyl)anthracene, and a symmetric molecule, {192}, at the solution-HOPG interface depends strongly on the components' solution concentrations and sample annealing history. The kinked alkadiyne side chain, {33}, packs optimally only with antiparallel aligned, {33} side chains. Thus, optimal packing of {33} side chains should assemble "{33} stripes" consisting of two adjacent {33,19} columns with interdigitated {33} chains. The aliphatic {19} side chain of {33,19} can pack with antiparallel aligned {19} side chains from {192} or from {33,19}. Thus, {33} stripes can incorporate as "guests" within {192} "host" monolayers. The composition and morphology of monolayers formed by drop casting solutions of {33,19} and {192} at 19 °C are dominated by assembly kinetics. Short {33} strips are immersed haphazardly in monolayers comprised mostly of {192}. Thermal annealing promotes fuller expression of {33,19}'s shape amphiphilicity and assembly of thermodynamically determined monolayers incorporating 1-D {33} stripes within a 2-D matrix of {192}. Larger solution mole fractions of {192} yield annealed monolayers with nearly constant {33} strip lengths, decreased {33} strip density, and increased {33} strip spacing.

Odd or even? Monolayer domain size depends on diyne position in alkadiynylanthracenes.

1,5-(Alkadiynyl)anthracenes self-assemble single component and multicomponent monolayers at the solution-HOPG interface. An alkadiynyl chain's kinked shape constrains the molecular structures with which it can close-pack. This affords rudimentary molecular recognition that has been used to direct self-assembly of 1-D patterned, multicomponent monolayers. The unit cell building blocks of single- and multicomponent alkadiynylanthracene monolayers repeat with high fidelity for 100s of nanometers along the side chain direction. Unit cell repeat fidelity along the orthogonal, anthracene column direction of the monolayer depends on diyne location within the side chain; even-position diyne side chains produce high fidelity of unit cell repeats and wider domain widths along the anthracene columns, whereas odd-position diyne side chains produce more frequent domain interfaces that disrupt the anthracene columns. Alkadiynylanthracene monolayers may be viewed as stacks of 1-D molecular tapes. 1-D tape molecular composition, sequence, and intratape side chain alignment are dictated by shape complementarity of the kinked alkadiynyl side chains. Stacking alignments of adjacent 1-D tapes are controlled by shape matching of tape peripheries and determine repeat fidelity along the anthracene columns. Tapes stacked with a constant intertape alignment comprise crystalline domains that repeat along the anthracene columns. The 1-D tapes formed by anthracenes with odd-position diynes have triangle wave peripheries that close-pack in multiple stacking alignments. This reduces unit cell repeat fidelity and decreases the widths of crystalline domains along the anthracene columns. Even-position diyne side chains form 1-D tapes with trapezoid wave peripheries that close-pack in only one stacking alignment. This generates higher stacking fidelity, larger domain widths, and fewer domain interfaces along the anthracene columns of even-position diyne monolayers. Even- and odd-position diyne monolayers exhibit comparable densities of interfaces between enantiotopic domains and between domains aligned along different graphite symmetry axes. These interfaces likely arise through collisions of independently nucleated/growing domains and persist for lack of kinetically competent pathways that interconvert or merge the domains.

Monolayer patterning using ketone dipoles.

The self-assembly of multi-component monolayers with designed patterns requires molecular recognition among components. Dipolar interactions have been found to influence morphologies of self-assembled monolayers and can affect molecular recognition functions. Ketone groups have large dipole moments (2.6 D) and are easily incorporated into molecules. The potential of ketone groups for dipolar patterning has been evaluated through synthesis of two 1,5-disubstituted anthracenes bearing mono-ketone side chains, STM characterization of monolayers self-assembled from their single and two component solutions and molecular mechanics simulations to determine their self-assembly energetics. The results reveal that (i) anthracenes bearing self-repulsive mono-ketone side chains assemble in an atypical monolayer morphology that establishes dipolar attraction, instead of repulsion, between ketones in adjacent side chains; (ii) pairs of anthracene molecules whose self-repulsive ketone side chains are dipolar complementary spontaneously assemble compositionally patterned monolayers, in which the two components segregate into neighboring, single component columns, driven by side chain dipolar interactions; (iii) compositionally patterned monolayers also assemble from dipolar complementary anthracene pairs that employ different dipolar groups (ketones or CF2 groups) in their side chains; (iv) the ketone group, with its larger dipole moment and size, provides comparable driving force for patterned monolayer formation to that of the smaller dipole, and smaller size, CF2 group.

Reactive capture of gold nanoparticles by strongly physisorbed monolayers on graphite.

Anthracene Diels Alder adducts (DAa) bearing two long side chains (H-(CH(2))(22)O(CH(2))(6)OCH(2)-) at the 1- and 5-positions form self-assembled monolayers (SAMs) at the phenyloctane-highly oriented pyrolytic graphite (HOPG) interface. The long DAa side chains promote strong physisorption of the monolayer to HOPG and maintain the monolayer morphology upon rinsing or incubation in ethanol and air-drying of the substrate. Incorporating a carboxylic acid group on the DAa core enables capture of 1-4 nm diameter gold nanoparticles (AuNPs) provided (i) the monolayer containing DAa-carboxylic acids is treated with Cu(2+) ions and (ii) the organic coating on the AuNP contains carboxylic acids (11-mercaptoundecanoic acid, MUA-AuNP). AuNP capture by the monolayer proceeds with formation of Cu(2+)-carboxylate coordination complexes. The captured AuNP appear as mono- and multi-layered clusters at high coverage on HOPG. The surface density of the captured AuNPs can be adjusted from AuNP multi-layers to isolated AuNPs by varying incubation times, MUA-AuNP concentration, the number density of carboxylic acids in the monolayer, the number of MUA per AuNP, and post-incubation treatments.

Patterned monolayer self-assembly programmed by side chain shape: four-component gratings.

A molecular recognition strategy based on alkadiyne side chain shape is used to self-assemble a four-component, 1D-patterned monolayer at the solution-HOPG interface. The designed monolayer unit cell contains six molecules and spans 23 nm × 1 nm. The unit cell's internal structure and packing are driven by complementary shapes and lengths of six different alkadiyne side chains. A solution of the four compounds on HOPG self-assembles monolayers (i) comprised, almost entirely, of the intended unit cell, (ii) exhibiting patterned domains spanning 10(4) nm(2), and (iii) which are sufficiently robust that patterned domains survive solvent rinsing and drying. The patterned monolayer affords 1D-feature spacings ranging from 3.3 to 23 nm. The results demonstrate the remarkable selectivity afforded by molecular recognition based on alkadiyne side chain shape and the ability to program highly complex 1D-patterns in self-assembled monolayers.

Tetris in monolayers: patterned self-assembly using side chain shape.

The "kinked" shapes of conjugated alkadiynes constrain chain packing in monolayers on HOPG. Centrally located diyne units permit assembly of 1,5-bis(alkadiyne)anthracene monolayers. Off-center diynes inhibit self-assembly. Shape matched pairs of off-center diyne chains direct self-assembly of compositionally patterned, two component monolayers.

Photo- and biophysical studies of lectin-conjugated fluorescent nanoparticles: reduced sensitivity in high density assays.

Lectin-conjugated, fluorescent silica nanoparticles (fNP) have been developed for carbohydrate-based histopathology evaluations of epithelial tissue biopsies. The fNP platform was selected for its enhanced emissive brightness compared to direct dye labeling. Carbohydrate microarray studies were performed to compare the carbohydrate selectivity of the mannose-recognizing lectin Concanavalin A (ConA) before and after conjugation to fluorescent silica nanoparticles (ConA-fNP). These studies revealed surprisingly low emission intensities upon staining with ConA-fNP compared to those with biotin-ConA/Cy3-streptavidin staining. A series of photophysical and biophysical characterizations of the fNP and ConA-fNP conjugates were performed to probe the low sensitivity from fNP in the microarray assays. Up to 1200 fluorescein (FL) and 80 tetramethylrhodamine (TR) dye molecules were incorporated into 46 nm diameter fNP, yielding emissive brightness values 400 and 35 times larger than the individual dye molecules, respectively. ConA lectin conjugated to carboxylic acid surface-modified nanoparticles covers 15-30% of the fNP surface. The CD spectra and mannose substrate selectivity of ConA conjugated to the fNP differed slightly compared to that of soluble ConA. Although, the high emissive brightness of fNP enhances detection sensitivity for samples with low analyte densities, large fNP diameters limit fNP recruitment and binding to samples with high analyte densities. The high analyte density and nearly two-dimensional target format of carbohydrate microarrays make probe size a critical parameter. In this application, fNP labels afford minimal sensitivity advantage compared to direct dye labeling.

Dipolar side chain control of monolayer morphology: symmetrically substituted 1,5-(mono- and diether) anthracenes at the solution-HOPG interface.

Scanning tunneling microscopy (STM) is used to determine the 2-D unit cell parameters of monolayers self-assembled by twelve symmetrical, 1,5-bis(linear aliphatic ether side chain) anthracenes at the solution-graphite interface. The standard morphology assembled by 1,5-bis(alkyloxymethyl) anthracenes consists of single-lamella domains containing columns of anthracene cores alternating with columns of interdigitated, aliphatic side chains. Adjacent side chains within the aliphatic columns adsorb in antiparallel orientations. The terminal methyl (omega-position) of each side chain lies in registration with the 2-positions of its two neighboring chains ((omega <--> 2)-packing). Anthracenes with diether side chains can generate repulsive or attractive dipole-dipole interactions between proximate ethers of adjacent aliphatic chains. Anthracenes bearing even length side chains with oxygens at the 2- and omega-1 positions or at the 3- and omega-2 positions do not assemble (omega <--> 2)-packed monolayers. Repulsive dipolar interactions between ethers in adjacent side chains raise the energy of (omega <--> 2) morphologies. These "self-repulsive" side chains drive assembly of (omega <--> l)- or (omega <--> 3)-packed morphologies, which enjoy stabilizing dipolar interactions between ethers in adjacent side chains. In stark contrast, anthracenes bearing odd length diether side chains assemble (omega <--> 2)-packed morphologies, regardless of whether adjacent chains suffer zero, one, or two sets of proximate dipole-dipole repulsions. The intrinsic energy gap from (omega <--> 2)- to non-(omega <--> 2)-packed morphologies of odd length side chain anthracenes is, apparently, larger than for even length side chain anthracenes. Overall, the twelve compounds self-assemble seven different morphologies. Distinguishing morphologies, understanding polymorphism within the monolayers, and evaluating the morphological consequences of side chain dipolar interactions is facilitated by viewing the monolayers as assemblies of 1-D, molecular tapes.

Self-assembly of patterned monolayers with nanometer features: molecular selection based on dipole interactions and chain length.

Patterned cocrystal monolayers self-assemble on HOPG in contact with solutions containing complementary pairs of 1,5-chain-substituted anthracene derivatives. Monolayer unit cells containing three or four molecules and spanning 9-11 nm are generated. The monolayers consist of alternating aromatic and aliphatic columns. The designs and dimensions of the cocrystal patterns (unit cells) are determined by (i) the preferred packing alignment of identical length side chains, (ii) the selectivity of each side chain for neighboring chains, (iii) the identities of the two side chains on each anthracene, and (iv) the 2D-chirality of 1,5-substituted anthracenes. The aliphatic columns form by interdigitation of identical length side chains arrayed in an antiparallel alignment, with the nth heavy atom of one side chain in registration with the (omega+2-n)th heavy atom of two adjacent chains ((omega <--> 2) packing). Adjacent side chains are attached, alternately, to anthracenes in one of the two flanking aromatic columns. The preference for (omega <--> 2) packing optimizes side-chain van der Waals interactions. The composition and fidelity of patterning in the cocrystal monolayers requires an additional source of "molecular recognition" in addition to side-chain length. Dipolar interactions, both attractive and repulsive, between ether groups in neighboring, (omega <--> 2) packed side chains, constitute a second recognition element needed for cocrystal self-assembly.

Nanowiring of a redox enzyme by metallized peptides.

A molecular assembly consisting of a redox enzyme, NADH peroxidase, a metallized double-helical peptide, and a gold nanoparticle immobilized onto a gold wire derivatized with a benzenedithiol compound, initiated and conducted redox signals in the presence of H(2)O(2) and NADH. The current generated by the binding of NADH, the electron donor, was transduced through the molecular assembly with apparently little loss of signal to the solution. The currents measured correlate to an electron transfer rate constant on the order of 3,000 s(-1) within each assembly. This electron transfer rate is two orders of magnitude higher than the endogenous electron transfer rate from NADH to the native enzyme, 27 s(-1). This rate indicates that the metallized peptide is in a conformation conducive for electron transfer and, in conjunction with the redox enzyme, can form effective conduits of electrical signals. This work demonstrates the feasibility of utilizing designed and highly efficient biomolecular assemblies for the production of ultra-sensitive, in-situ biosensors.

Photothermal readout of surface-arrayed proteins: attomole detection levels with gold nanoparticle visualization.

Transverse photothermal beam deflection (tPBD) is used to detect and quantify proteins arrayed on slides. The slides are "read" using an argon-ion excitation source. Optical absorption cross-sections of most proteins are too small for submonolayer coverages to produce thermal gradients of sufficient magnitude for detection using tPBD. Thus, surface-arrayed proteins are stained using mercaptoalkanoic acid coated gold nanoparticles (maa-AuNP). The large optical cross-sections of AuNP combined with electrolyte-induced AuNP aggregation afford a highly sensitive method for protein detection. Following maa-AuNP staining, the tPBD signal varies linearly with the amount of protein (Neutravidin) spotted on the slide surface: from 0.001 to 1.0 monolayer of protein. In a single 0.7 mm diameter array spot, the tPBD detection limit is 33 amol of Neutravidin or fewer than 55 protein molecules per microm2. Despite the nonspecific nature of interactions between maa-AuNP and proteins, significant variations in protein staining efficacy are observed. The factors controlling staining are not elucidated in detail, but there is a correlation between protein pI and protein staining. Proteins with pI approximately 6 are more effectively visualized by maa-AuNp than are more acidic or more basic proteins. The influence of AuNP diameter and mercaptoalkanoic acid chain length on protein staining and selectivity is investigated. The results demonstrate that AuNP staining coupled with tPBD detection constitutes a sensitive and practical method for probing protein arrays.

Scanning tunneling microscopy of prochiral anthracene derivatives on graphite: chain length effects on monolayer morphology.

The morphology of monolayers formed upon adsorption of prochiral 1,5-substituted anthracene derivatives on highly oriented pyrolytic graphite is investigated using scanning tunneling microscopy at the liquid-solid interface. The adsorption orientation of these prochiral anthracene derivatives positions one of their enantiotopic faces in contact with the graphite. The molecules adsorb in rows with contact between adjacent anthracenes. The anthracene side chains extend perpendicular to the direction of the row repeat. All molecules within a single row adsorb via the same enantiotopic face. Anthracenes with side chains containing an even number of non-hydrogenic atoms (C, S) form monolayers in which molecules in adjacent rows adsorb via opposite enantiotopic faces. Anthracenes with side chains that contain an odd number of non-hydrogenic atoms form two-dimensional chiral domains in which all rows contain molecules adsorbed via the same enantiotopic face. This chain length effect on monolayer morphology represents a generalized example of structural effects previously observed in alkanoic acid monolayers formed on HOPG. The variation of the STM current with position in the vicinity of the anthracenes indicates that the highest occupied molecular orbital is the predominant mediator of tunneling for the aromatic group.

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study.

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

Hole transfer in a C-shaped molecule: conformational freedom versus solvent-mediated coupling.

The electronic coupling matrix elements attending the charge separation reactions of a C-shaped molecule containing an excited pyrene as the electron acceptor and a dimethylaniline as the donor are determined in aromatic, ether, and ester solvents. Band shape analyses of the charge-transfer emission spectra (CT --> S(0)) provide values of the reaction free energy, the solvent reorganization energy, and the vibrational reorganization energy in each solvent. The free energy for charge separation in benzene and toluene solvents is independently determined from the excited state equilibrium established between the locally excited pyrene S(1) state and the charge-transfer state. Analyses of the charge separation kinetics using the spectroscopically determined reorganization energies and reaction free energies indicate that the electronic coupling is solvent independent, despite the presence of a cleft between the donor and acceptor. Hence, solvent molecules are not involved in the coupling pathway. The orientations of the donor and acceptor units, relative to the spacer, are not rigidly constrained, and their torsional motions decrease solvent access to the cleft. Generalized Mulliken-Hush calculations show that rotation of the pyrene group about the bond connecting it to the spacer greatly modulates the magnitude of through-space coupling between the S(1) and CT states. The relationship between the torsional dynamics and the electron-transfer dynamics is discussed.