Rectification in Molecular Tunneling Junctions Based on Alkanethiolates with Bipyridine-Metal Complexes.

This paper addresses the mechanism for rectification in molecular tunneling junctions based on alkanethiolates terminated by a bipyridine group complexed with a metal ion, that is, having the structure AuTS-S(CH2)11BIPY-MCl2 (where M = Co or Cu) with a eutectic indium-gallium alloy top contact (EGaIn, 75.5% Ga 24.5% In). Here, AuTS-S(CH2)11BIPY is a self-assembled monolayer (SAM) of an alkanethiolate with 4-methyl-2,2'-bipyridine (BIPY) head groups, on template-stripped gold (AuTS). When the SAM is exposed to cobalt(II) chloride, SAMs of the form AuTS-S(CH2)11BIPY-CoCl2 rectify current with a rectification ratio of r+ = 82.0 at ±1.0 V. The rectification, however, disappears (r+ = 1.0) when the SAM is exposed to copper(II) chloride instead of cobalt. We draw the following conclusions from our experimental results: (i) AuTS-S(CH2)11BIPY-CoCl2 junctions rectify current because only at positive bias (+1.0 V) is there an accessible molecular orbital (the LUMO) on the BIPY-CoCl2 moiety, while at negative bias (-1.0 V), neither the energy level of the HOMO or the LUMO lies between the Fermi levels of the electrodes. (ii) AuTS-S(CH2)11BIPY-CuCl2 junctions do not rectify current because there is an accessible molecular orbital on the BIPY-CuCl2 moiety at both negative and positive bias (the HOMO is accessible at negative bias, and the LUMO is accessible at positive bias). The difference in accessibility of the HOMO levels at -1.0 V causes charge transfer-at negative bias-to take place via Fowler-Nordheim tunneling in BIPY-CoCl2 junctions, and via direct tunneling in BIPY-CuCl2 junctions. This difference in tunneling mechanism at negative bias is the origin of the difference in rectification ratio between BIPY-CoCl2 and BIPY-CuCl2 junctions.

Conformation, and Charge Tunneling through Molecules in SAMs.

This paper demonstrates that the molecular conformation (in addition to the composition and structure) of molecules making up self-assembled monolayers (SAMs) influences the rates of charge tunneling (CT) through them, in molecular junctions of the form AuTS/S(CH2)2CONR1R2//Ga2O3/EGaIn, where R1 and R2 are alkyl chains of different length. The lengths of chains R1 and R2 were selected to influence the conformations and conformational homogeneity of the molecules in the monolayer. The conformations of the molecules influence the thickness of the monolayer (i.e. tunneling barrier width) and their rectification ratios at ±1.0 V. When R1 = H, the molecules are well ordered and exist predominantly in trans-extended conformations. When R1 is an alkyl group (e.g., R1 ≠ H), however, their conformations can no longer be all-trans-extended, and the molecules adopt more gauche dihedral angles. This change in the type of conformation decreases the conformational order and influences the rates of tunneling. When R1 = R2, the rates of CT decrease (up to 6.3×), relative to rates of CT observed through SAMs having the same total chain lengths, or thicknesses, when R1 = H. When R1 ≠ H ≠ R2, there is a weaker correlation (relative to that when R1 = H or R1 = R2) between current density and chain length or monolayer thickness, and in some cases the rates of CT through SAMs made from molecules with different R2 groups are different, even when the thicknesses of the SAMs (as determined by XPS) are the same. These results indicate that the thickness of a monolayer composed of insulating, amide-containing alkanethiols does not solely determine the rate of CT, and rates of charge tunneling are influenced by the conformation of the molecules making up the junction.

Characterizing Chelation at Surfaces by Charge Tunneling.

This paper describes a surface analysis technique that uses the "EGaIn junction" to measure tunneling current densities (J(V), amps/cm2) through self-assembled monolayers (SAMs) terminated in a chelating group and incorporating different transition metal ions. Comparisons of J(V) measurements between bare chelating groups and chelates are used to characterize the composition of the SAM and infer the dissociation constant (Kd, mol/L), as well as kinetic rate constants (koff, L/mol·s; kon, 1/s) of the reversible chelate-metal reaction. To demonstrate the concept, SAMs of 11-(4-methyl-2,2'-bipyrid-4'-yl (bpy))undecanethiol (HS(CH2)11bpy) were incubated within ethanol solutions of metal salts. After rinsing and drying the surface, measurements of current as a function of incubation time and concentration in solution are used to infer koff, kon, and Kd. X-ray photoelectron spectroscopy (XPS) provides an independent measure of surface composition to confirm inferences from J(V) measurements. Our experiments establish that (i) bound metal ions are stable to the rinsing step as long as the rinsing time, τrinse ≪ 1koff; (ii) the bound metal ions increase the current density at the negative bias and reduce the rectification observed with free bpy terminal groups; (iii) the current density as a function of the concentration of metal ions in solution follows a sigmoidal curve; and (iv) the values of Kd measured using J(V) are comparable to those measured using XPS, but larger than those measured in solution. The EGaIn junction, thus, provides a new tool for the analysis of the composition of the surfaces that undergo reversible chemical reactions with species in solution.

Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life.

How simple chemical reactions self-assembled into complex, robust networks at the origin of life is unknown. This general problem-self-assembly of dissipative molecular networks-is also important in understanding the growth of complexity from simplicity in molecular and biomolecular systems. Here, we describe how heterogeneity in the composition of a small network of oscillatory organic reactions can sustain (rather than stop) these oscillations, when homogeneity in their composition does not. Specifically, multiple reactants in an amide-forming network sustain oscillation when the environment (here, the space velocity) changes, while homogeneous networks-those with fewer reactants-do not. Remarkably, a mixture of two reactants of different structure-neither of which produces oscillations individually-oscillates when combined. These results demonstrate that molecular heterogeneity present in mixtures of reactants can promote rather than suppress complex behaviors.

Dipole-Induced Rectification Across AgTS/SAM//Ga2O3/EGaIn Junctions.

This Article describes the relationship between molecular structure, and the rectification of tunneling current, in tunneling junctions based on self-assembled monolayers (SAMs). Molecular dipoles from simple organic functional groups (amide, urea, and thiourea) were introduced into junctions with the structure AgTS/S(CH2) nR(CH2) mCH3//Ga2O3/EGaIn. Here, R is an n-alkyl fragment (-CH2-)2 or 3, an amide group (either -CONH- or -NHCO-), a urea group (-NHCONH-), or a thiourea group (-NHCSNH-). The amide, urea, or thiourea groups introduce a localized electric dipole moment into the SAM and change the polarizability of that section of the SAM, but do not produce large, electronically delocalized groups or change other aspects of the tunneling barrier. This local change in electronic properties correlates with a statistically significant, but not large, rectification of current ( r+) at ±1.0 V (up to r+ ≈ 20). The results of this work demonstrate that the simplest form of rectification of current at ±1.0 V, in EGaIn junctions, is an interfacial effect, and is caused by a change in the work function of the SAM-modified silver electrode due to the proximity of the dipole associated with the amide (or related) group, and not to a change in the width or mean height of the tunneling barrier.

Autocatalytic Cycles in a Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction.

This work describes the autocatalytic copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction between tripropargylamine and 2-azidoethanol in the presence of Cu(II) salts. The product of this reaction, tris-(hydroxyethyltriazolylmethyl)amine (N(C3N3)3), accelerates the cycloaddition reaction (and thus its own production) by two mechanisms: (i) by coordinating Cu(II) and promoting its reduction to Cu(I) and (ii) by enhancing the catalytic reactivity of Cu(I) in the cycloaddition step. Because of the cooperation of these two processes, a rate enhancement of >400× is observed over the course of the reaction. The kinetic profile of the autocatalysis can be controlled by using different azides and alkynes or ligands (e.g., ammonia) for Cu(II). When carried out in a layer of 1% agarose gel, and initiated by ascorbic acid, this autocatalytic reaction generates an autocatalytic front. This system is prototypical of autocatalytic reactions where the formation of a product, which acts as a ligand for a catalytic metal ion, enhances the production and activity of the catalyst.

Fluorescence of Cyclopropenium Ion Derivatives.

The synthesis of cyclopropenium-substituted amino compounds and analysis of their photophysical properties is described. Systematic structural modifications of these derivatives lead to measurable and predictable changes in molar extinction coefficients, quantum yields, and Stokes shifts. Using time-dependent density functional theory (TD-DFT) calculations, the origin of these trends was traced to internal charge transfer (ICT) coupled with ensuing structural reorganization for select naphthalene functionalized derivatives. Associated with this structural reorganization was an inward gearing of the cyclopropenium ring and twisting of the peri-NMe2 group into coplanarity with the naphthalene ring system. Further, reinforcement of an intramolecular H-bond (IMHB) in the excited state of these derivatives alludes to the importance of photoinduced H-bonding in this new class of cyclopropenium based fluorophores.

A Mechanistic Model for the Aziridine Aldehyde-Driven Macrocyclization of Peptides.

Aziridine aldehyde-driven macrocyclization of peptides is a powerful tool for the construction of biologically active macrocycles. While this process has been used to generate diverse collections of cyclic molecules, its mechanistic underpinnings have remained unclear. To enable progress in this area we have carried out a mechanistic study, which suggests that the cyclization owes its efficiency to a combination of electrostatic attraction between the termini of a nitrilium ion intermediate and intramolecular hydrogen bonding. Our model adequately explains the experimentally observed trends, including diastereoselectivity, and should facilitate the development of other macrocyclization reactions.

Synthesis, Theoretical Analysis, and Experimental pKa Determination of a Fluorescent, Nonsymmetric, In-Out Proton Sponge.

Herein, we report the synthesis and theoretical investigation of a nonsymmetric bis(diisopropylamino)cyclopropenimine (DAC)-functionalized proton sponge derivative, coined the "Janus" sponge. The reported sponge was isolated as a monoprotonated salt, though no intramolecular hydrogen bond was observed. Homodesmotic equations supported the absence of a N-HN intramolecular hydrogen bond and a relatively low freebase strain, while DFT calculations and X-ray crystallography revealed the presence of a hydrogen bond to the Cl(-) counterion. Associated with this fact was the rare in-out geometry of the basic nitrogens, which represents the first such instance in a proton sponge not having an ortho-substituent and/or being in a protonated state. Furthermore, NLP donation into the cyclopropenium cation was found to stabilize this unprecedented in-out geometry. The measured pKa was determined to be 23.8, in good agreement with the computed value of 23.9. Lastly, the Janus sponge was found to have fluorescent properties both in the solid state and in solution, which notably represents the first example of a cyclopropenimine-based fluorescent organic compound.

Phase-Transfer Catalysis via a Proton Sponge: A Bifunctional Role for Biscyclopropenimine.

The use of a bis(diisopropylamino)cyclopropenimine-substituted bis-protonated proton sponge as a bifunctional phase-transfer catalyst is reported. Experimental studies and DFT calculations suggest it operates simultaneously as a hydrogen bond donor and a phase-transfer catalyst, facilitating the movement of charged intermediates from the interface to the organic phase via favorable partitioning of hydrophilic/hydrophobic surface areas, resulting in high catalytic activity.

Synthesis of Chiral Piperazinones Using Amphoteric Aziridine Aldehyde Dimers and Functionalized Isocyanides.

We have evaluated a range of functionalized isocyanides in the aziridine aldehyde-driven multicomponent synthesis of piperazinones. High diasteroselectivity for each isocyanide was observed. A theoretical evaluation of the reaction course corroborates the experimental data. Moreover, the reactivity of cis- and trans-configured aziridine aldehyde dimers has been compared. This study further probes the dimer-driven mechanism of cyclization and enables an efficient access to a wide range of chiral piperazinones bearing functionalized side chains.

Hydroxyproline-derived pseudoenantiomeric [2.2.1] bicyclic phosphines: asymmetric synthesis of (+)- and (-)-pyrrolines.

We have prepared two new diastereoisomeric 2-aza-5-phosphabicyclo[2.2.1]heptanes from naturally occurring trans-4-hydroxy-L-proline in six chemical operations. These syntheses are concise and highly efficient, with straightforward purification. When we used these chiral phosphines as catalysts for reactions of γ-substituted allenoates with imines, we obtained enantiomerically enriched pyrrolines in good yields with excellent enantioselectivities. These two diastereoisomeric phosphines functioned as pseudoenantiomers, providing their chiral pyrrolines with opposite absolute configurations.

Synthesis and theoretical investigation of a 1,8-bis(bis(diisopropylamino)cyclopropeniminyl)naphthalene proton sponge derivative.

We report herein the synthesis and characterization of a new proton sponge derivative, 1,8-bis(bis(diisopropylamino)cyclopropeniminyl)naphthalene 4 (DACN), as well as its bis-protonated counterpart 6. A crystal structure of 6 is presented, along with variable temperature (1)H NMR data on the BF4(-) salt (6⋅BF4). DFT calculations were performed to investigate the structure of the monoprotonated species 7 and to gain insight into the structural and electronic nature of all three species. The proton affinity (PA) of 4, calculated at the B3LYP/6-311G++(d,p)//B3LYP/6-31G(d,p) level, taking into account thermal corrections from the B3LYP/6-31G(d,p) method, was 282.3 kcal mol(-1), while its pKa was estimated at 27.0. NICS calculations were performed to examine the changes in aromaticity within these systems upon each successive protonation. Lastly, homodesmotic reaction schemes were used in order to estimate the factors contributing to the strong PA predicted for 4.

Shifting the energy landscape of multicomponent reactions using aziridine aldehyde dimers: a mechanistic study.

A multicomponent reaction between an aziridine aldehyde dimer, isocyanide, and l-proline to afford a chiral piperazinone was studied to gain insight into the stereodetermining and rate-limiting steps of the reaction. The stereochemistry of the reaction was found to be determined by isocyanide addition, while the rate-limiting step was found to deviate from traditional isocyanide-based multicomponent reactions. A first-order rate dependence on aziridine aldehyde dimer and a zero-order rate dependence on all other reagents have been obtained. Computations at the MPWPW91/6-31G(d) level supported the experimental kinetic results and provide insight into the overall mechanism and the factors contributing to stereochemical induction. These factors are similar to traditional isocyanide-based multicomponent reactions, such as the Ugi reaction. The computations revealed that selective formation of a Z-iminium ion plays a key role in controlling the stereoselectivity of isocyanide addition, and the carboxylate group of l-proline mediates stereofacial addition. These conclusions are expected to be applicable to a wide range of reported stereoselective Ugi reactions and provide a basis for understanding the related macrocyclization of peptides with aziridine aldehydes.

A coordination compound of Ge(0) stabilized by a diiminopyridine ligand.

Reduction of the cationic Ge(II) complex [dimpyrGeCl][GeCl3] (dimpyr=2,6-(ArN=CMe)2NC5H3, Ar=2,6-iPr2C6H3) with potassium graphite in benzene affords an air sensitive, dark green compound of Ge(0), [dimpyrGe], which is stabilized by a bis(imino)pyridine platform. This compound is the first example of a complex of a zero-valent Group 14 element that does not contain a carbene or carbenoid ligand. This species has a singlet ground state. DFT studies revealed partial delocalization of one of the Ge lone pairs over the π*(C=N) orbitals of the imines. This delocalization results in a partial multiple-bond character between the Ge atom and imine nitrogen atoms, a fact supported by the X-ray crystallography and IR spectroscopy data.

A computational study of the copper(II)-catalyzed enantioselective intramolecular aminooxygenation of alkenes.

The origin of the enantioselectivity in the [Cu(R,R)-Ph-box](OTf)2-catalyzed intramolecular aminooxygenation of N-sulfonyl-2-allylanilines and 4-pentenylsulfonamides to afford chiral indolines and pyrrolidines, respectively, was investigated using density functional theory (DFT) calculations. The pyrrolidine-forming transition-state model for the major enantiomer involves a chairlike seven-membered cyclization transition state with a distorted square-planar copper center, while the transition-state model for the minor enantiomer was found to have a boatlike cyclization geometry having a distorted tetrahedral geometry about the copper center. Similar copper-geometry trends were observed in the chiral indoline-forming reactions. These models were found to be qualitatively consistent with experimental results and allow for rationalization of how substitution on the substrate backbone and N-sulfonyl substituent affect the level of enantioselectivity in these and related copper(II)-catalyzed enantioselective reactions.

Charge Transport Measured Using the EGaIn Junction through Self-Assembled Monolayers Immersed in Organic Liquids.

This paper describes measurements of charge transport by tunneling through molecular junctions comprising a self-assembled monolayer (SAM) supported by a template-stripped metal bottom electrode (MTS), which has been immersed in an organic liquid and contacted by a conical Ga2O3/EGaIn top electrode. These junctions formed in organic liquids are robust; they show stabilities and yields similar to those formed in air. We formed junctions under seven external environments: (I) air, (II) perfluorocarbons, (III) linear hydrocarbons, (IV) cyclic hydrocarbons, (V) aromatic compounds, (VI) large, irregularly shaped hydrocarbons, and (VII) dimethyl siloxanes. Several different lengths of SAMs of n-alkanethiolates, S(CH2)n-1CH3 with n = 4-18, and two different kinds of bottom electrodes (AgTS or AuTS) are employed to assess the mechanism underlying the observed changes in tunneling currents. Measurements of current density through junctions immersed in perfluorocarbons (II) are comparable to junctions measured in air. Junctions immersed in other organic liquids show reductions in the values of current density, compared to the values in air, ranging from 1 (III) to 5 orders of magnitude (IV). We interpret the most plausible mechanism for these reductions in current densities to be an increase in the length of the tunneling pathway, reflecting the formation of thin (0.5-1.5 nm) liquid films at the interface between the SAM and the Ga2O3/EGaIn electrode. Remarkably, the thickness of the liquid film─estimated by the simplified Simmons model, measurements of electrical breakdown of the junction, and simulations of molecular dynamics─is consistent with the existing observations of structured liquid layers that form between two flat interfaces from measurements obtained by the surface force apparatus. These results suggest the use of the EGaIn junction and measurements of charge transport by tunneling as a new form of surface analysis, with the applications in the study of near-surface, weak, molecular interactions and the behavior of liquid films adjacent to non-polar interfaces.

Evidence for alkene cis-aminocupration, an aminooxygenation case study: kinetics, EPR spectroscopy, and DFT calculations.

Alkene difunctionalization reactions are important in organic synthesis. We have recently shown that copper(II) complexes can promote and catalyze intramolecular alkene aminooxygenation, carboamination, and diamination reactions. In this contribution, we report a combined experimental and theoretical examination of the mechanism of the copper(II)-promoted olefin aminooxygenation reaction. Kinetics experiments revealed a mechanistic pathway involving an equilibrium reaction between a copper(II) carboxylate complex and the γ-alkenyl sulfonamide substrate and a rate-limiting intramolecular cis-addition of N-Cu across the olefin. Kinetic isotope effect studies support that the cis-aminocupration is the rate-determining step. UV/Vis spectra support a role for the base in the break-up of copper(II) carboxylate dimer to monomeric species. Electron paramagnetic resonance (EPR) spectra provide evidence for a kinetically competent N-Cu intermediate with a Cu(II) oxidation state. Due to the highly similar stereochemical and reactivity trends among the Cu(II)-promoted and catalyzed alkene difunctionalization reactions we have developed, the cis-aminocupration mechanism can reasonably be generalized across the reaction class. The methods and findings disclosed in this report should also prove valuable to the mechanism analysis and optimization of other copper(II) carboxylate promoted reactions, especially those that take place in aprotic organic solvents.

Controlled Hysteresis of Conductance in Molecular Tunneling Junctions.

The problem this paper addresses is the origin of the hysteretic behavior in two-terminal molecular junctions made from an EGaIn electrode and self-assembled monolayers of alkanethiolates terminated in chelates (transition metal dichlorides complexed with 2,2'-bipyridine; BIPY-MCl2). The hysteresis of conductance displayed by these BIPY-MCl2 junctions changes in magnitude depending on the identity of the metal ion (M) and the window of the applied voltage across the junction. The hysteretic behavior of conductance in these junctions appears only in an incoherent (Fowler-Nordheim) tunneling regime. When the complexed metal ion is Mn(II), Fe(II), Co(II), or Ni(II), both incoherent tunneling and hysteresis are observed for a voltage range between +1.0 V and -1.0 V. When the metal ion is Cr(II) or Cu(II), however, only resonant (one-step) tunneling is observed, and the junctions exhibit no hysteresis and do not enter the incoherent tunneling regime. Using this correlation, the conductance characteristics of BIPY-MCl2 junctions can be controlled. This voltage-induced change of conductance demonstrates a simple, fast, and reversible way (i.e., by changing the applied voltage) to modulate conductance in molecular tunneling junctions.

From bifunctional to trifunctional (tricomponent nucleophile-transition metal-lewis acid) catalysis: the catalytic, enantioselective α-fluorination of acid chlorides.

We report in full detail our studies on the catalytic, asymmetric α-fluorination of acid chlorides, a practical method that produces an array of α-fluorocarboxylic acid derivatives in which improved yield and virtually complete enantioselectivity are controlled through electrophilic fluorination of a ketene enolate intermediate. We discovered, for the first time, that a third catalyst, a Lewis acidic lithium salt, could be introduced into a dually activated system to amplify yields of aliphatic products, primarily through activation of the fluorinating agent. Through our mechanistic studies (based on kinetic data, isotopic labeling, spectroscopic measurements, and theoretical calculations) we were able to utilize our understanding of this "trifunctional" reaction to optimize the conditions and obtain new products in good yield and excellent enantioselectivity.