Interface and molecular electronic structure vs tunneling characteristics of CH3- and CF3-terminated thiol monolayers on Au(111)

By means of density functional theory calculations, we investigate work functions, energy level alignments, charge transfers, and tunneling characteristics of CH3- and CF3-terminated alkane- and diphenylthiol monolayers on Au(111). While the alignments of the energy levels and the charge transfers at the metal-molecule interface are found to be determined by the value of the clean Au surface work function relative to the HOMO ionization potential (IP) at the thiolate end of the monolayer, the change of work function for the modified Au(111) surface is dominated by the properties of the thiolate monolayer, including the character, saturated or conjugated, of the molecule and the chemical nature and orientation of the terminal group. The tunneling currents through the adsorbed molecular monolayers are calculated using the Tersoff-Hamann approach. The computed difference between the I-V characteristics for the CH3- and CF3-terminated alkanethiol monolayers agree well with available experimental data. The energy barrier at the metal-molecule interface, the molecular electronic structure, and the IP of the terminal group are the key parameters which determine the tunneling properties.     

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.     

Synthesis and stability of monolayer-protected Au38 clusters

A synthesis strategy to obtain monodisperse hexanethiolate-protected Au38 clusters based on their resistance to etching upon exposure to a hyperexcess of thiol is reported. The reduction time in the standard Brust-Schiffrin two-phase synthesis was optimized such that Au38 were the only clusters that were fully passivated by the thiol monolayer which leaves larger particles vulnerable to etching by excess thiol. The isolated Au38 was characterized by mass spectrometry, thermogravimetric analysis, optical spectroscopy, and electrochemical techniques giving Au38(SC6)22 as the molecular formula for the cluster. These ultrasmall Au clusters behave analogously to molecules with a wide energy gap between occupied (HOMO) and unoccupied levels (LUMO) and undergo single-electron charging at room temperature in electrochemical experiments. Electrochemistry provides an elegant means to study the electronic structure and the chemical stability of the clusters at different charge states. We used cyclic voltammetry and scanning electrochemical microscopy to unequivocally demonstrate that Au38 can be reversibly oxidized to charge states z = +1 or +2; however, reduction to z = -1 leads to desorption of the protecting thiolate monolayer. Although this reductive desorption of thiol from the cluster surface is superficially analogous to electrochemical desorption of planar self-assembled monolayers (SAMs) from macroscopic electrodes, the molecular details of the process are likely to be complicated based on the current view that the thiolate monolayer in clusters is in fact composed of polymeric Au-S complexes.     

Adsorption of thiols on the Pd(111) surface: a first principles study

Using density functional theory formalism, we have investigated the adsorption behavior of thiols on the Pd(111) surface. Two different thiol molecules, viz. (a) methane thiol and (b) thiophene 2-thiol (TSH), were used as model adsorbates for this purpose. The results revealed that whereas the methane thiol molecule undergoes spontaneous dissociative chemisorption onto the palladium surface, the adsorption of the thiophene 2-thiol molecule does not involve cleavage of the S-H bond, leading to weak interaction energy or physisorption. The variation in the adsorption behavior has been explained based on the difference in the electronic environment of the terminal sulfur atom. The nature of binding at the interface has been analyzed through calculation of the partial density of states of the sulfur atom at the interface.     

Thiol and thiolate bond formation of ferrocene-1,1-dithiol to a Ag(111) surface

Using density functional calculations, we show that the adsorption of ferrocene dithiol on the Ag(111) surface is remarkably flexible, i.e., a large number of different configurations have binding energies that differ by less than 0.1 eV per molecule. The thiolate bond is slightly favored over the thiol bond (by less than 0.1 eV) but may not be formed due to considerable activation barriers. Electronically, we found that the thiolate bound molecule is conducting, whereas thiol bonds turn it into semiconducting.     

Electron exchange involving a sulfur-stabilized ruthenium radical cation

Half-sandwich Ru(II) amine, thiol, and thiolate complexes were prepared and characterized by X-ray crystallography. The thiol and amine complexes react slowly with acetonitrile to give free thiol or amine and the acetonitrile complex. With the thiol complex, the reaction is dissociative. The thiolate complex has been oxidized to its Ru(III) radical cation and the solution EPR spectrum of that radical cation recorded. Cobaltocene reduces the thiol complex to the thiolate complex. The 1H and 31P NMR signals of the thiolate complex in acetonitrile become very broad whenever the thiolate and thiol complexes are present simultaneously. The line broadening is primarily due to electron exchange between the thiolate complex and its radical cation; the latter is generated by an unfavorable redox equilibrium between the thiol and thiolate complexes. Pyramidal inversion of sulfur in the thiol complex is fast at room temperature but slow at lower temperatures; major and minor conformers of the thiol complex were observed by 31P NMR at -98 degrees C in CD2Cl2.     

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].     

Ferrocene-1,1'-dithiol as molecular wire between Ag electrodes: the role of surface defects

The interaction of ferrocene-1,1(')-dithiol (FDT) with two parallel Ag(111) surfaces has been theoretically studied at density-functional level. The effect of surface defects on the energetic and electronic structure was investigated. The electronic transport properties are studied with the nonequilibrium Green's function approach. The adsorption geometry has a strong effect on the electronic levels and conductivity. The presence of point defects strongly enhances the molecule-surface interaction but has a surprisingly small effect on the density of states near the Fermi energy. The FDT-surface bond is particularly strong near terraces or steps and leads to significant shifts of the molecular orbitals relative to the gas phase. For all considered defect types except the single adatom the electronic conductivity through the FDT molecule is decreased compared to adsorption on perfect surfaces.     

Effects of end group functionalization and level alignment on electron transport in molecular devices

The effect of metal-molecule coupling on electron transport is examined in the prototypical case of alkane chains sandwiched between gold contacts and bridged by either amine or thiol groups. The results show that end group functionalization plays a crucial role in controlling electron transport, and that the symmetries and spatial extent of orbitals near the Fermi level control the conductivity rather than the strength of the bonding. For amine/Au and thiol/Au junctions, a crossover in conductivity with increasing bias is predicted.     

Effect of coverage and defects on the adsorption of propanethiol on Au(111) surface: a theoretical study

Periodic density functional calculations have been carried out to investigate both the thiol adsorption on Au(111) surface and the reaction mechanism for the formation of the self-assembled monolayers, taking propanethiol as a representative example. The effect of coverage and surface defects (adatoms and vacancies) has been analyzed. It is found that the most stable physisorption (undissociated) site is an adatom site, whereas the chemisorption site for the thiol is a vacancy site or protrusion consisting of a pair of adatoms, followed by one adatom site. The results point out that the thiolate self-assembled monolayer adsorption process occurs preferentially on step edges.     

Molecular binding at gold transport interfaces. IV. Thiol chemisorption

Alkene thiol/coinage metal molecular interfaces are relatively easy to make, and can result in well-ordered self-assembled monolayer films. The energetics of such formation is complex-differing experimental and theoretical accounts have focused on the nature of the binding, the energetics via different pathways (thiol radical, thiol or thiolate) and the geometry of binding. We report density functional theory calculations on a four atom gold cluster interacting with different (alkane, alkene, alkyne) thiolates. We find thiolate addition to be strongly exoergic, thiol radical to be roughly half as favorable, and thiol to be slightly favorable. We also find that the S-H bond can remain when the thiol attaches to the gold cluster, formally resulting in increased coordination on the sulfur atom.     

Dynamics and extent of ligand exchange depend on electronic charge of metal nanoparticles

Both the rate and extent of ligand place exchange reactions between the hexanethiolate monolayer of Au(140) monolayer protected clusters (C6 MPCs) and dissolved 6-mercapto-1-hexanol thiol (HOC6SH) increase with increasing positive electronic charge on the Au cluster core. The rate constant of the ligand place exchange, taken at the early stage of the exchange, is increased by ca. 2-fold for reaction of +3 charged Au(140) cores as compared to neutral ones. The initially exchanged ligands are thought to reside mainly on edge and vertex sites of the Au(140) core, where the lability of the slightly more ionic Au[bond]S bonds there becomes further enhanced by removing electrons from the core. The reactions slow markedly after 35-50% of the original ligands have been replaced, continuing at a much slower pace for some time to reach an apparent reaction equilibrium. On +2 charged Au(140) cores, 85% of the C6 ligands have been exchanged with HOC(6)H(12)SH after 20 h. The slower phase of the reaction includes exchange of thiolate ligands on terrace lattice sites most of which--owing to the small sizes of the nanoparticle's Au(111) faces--are no more than one Au atom row removed from the nanoparticle edge sites. This slower exchange, the extent of which is also enhanced by positively charging the core, occurs either by intramolecular place exchange with edge sites that subsequently place-exchange with solution thiol or by direct place-exchange with solution thiol. Acid-base studies show that thiolate is more reactive in place exchange reactions than the corresponding thiol.     

Surface/interface electronic structure in C(60) anchored aminothiolate self-assembled monolayer: an approach to molecular electronics

Electronic structure in self-assembled monolayers (SAMs) of C(60) anchored 11-amino-1-undecane thiol (C(60)-11-AUT) on Au(111) was studied by means of ultraviolet photoelectron spectroscopy and hybrid density functional theory calculations. Valence band features of the molecular conformation revealed the interface electronic structure to be dominated by sigma(S-Au), localized at the thiolate anchor to Au. Formation of a localized covalent bond as a result of hybridization between N P(z) orbital of -NH(2) group of the thiolate SAM and the pi level of C(60) resulted in a symmetry change from I(h) in C(60) to C1 in C(60)-11-AUT SAM. Appearance of low, but finite amplitude surface electronic states of bonded C(60), much beyond the Fermi level, ruled out Au-C(60) end group contact. The band gap E(g) of the SAM, determined to be 2.7 eV, was drastically reduced from the insulating alkanethiol SAMs ( approximately 8.0 eV) and fell intermediate between the C(60) ground state (N electrons, 1.6 eV) and C(60) solid (N+/-1 electrons, 3.7 eV).     

Correlation between HOMO alignment and contact resistance in molecular junctions: aromatic thiols versus aromatic isocyanides

Understanding electron transport in metal-molecule-metal (MMM) junctions is of great importance for the advancement of molecular electronics. Critical factors that determine conductivity in a MMM junction include the nature of metal-molecule contacts and the electronic structure of the molecular backbone. We have studied the electronic transport property and the valence electronic structure on rigid, conjugated oligoacenes of increasing length with either thiol (-S) or isocyanide (-CN) linkers using conducting probe atomic force microscopy (CP-AFM) and ultraviolet photoelectron spectroscopy (UPS). We find that for these conjugated systems the Au-CN contact is more resistive than Au-S. The difference in contact resistance correlates with UPS measurements that show the highest-occupied molecular orbital (HOMO) of the isocyanide series is lower in energy (relative to the Fermi level of Au) than the HOMO of the thiol series, indicating the presence of a higher tunneling barrier at the contact for the isocyanide-linked molecules. By contrast, the difference in the HOMO positions for the two series of molecules does not appear to affect the length dependence of the junction resistance (i.e., the beta value = 0.5 A-1).     

Electron transport across the alkanethiol self-assembled monolayer/Au(111) interface: role of the chemical anchor

Alkanethiol self-assembled monolayers (SAMs) on Au(111) are model systems for molecular electronics. We probe the role of the chemisorption bond on electron dynamics at the SAM/Au interface using time-resolved two-photon photoemission. Formation of the Au-S bond is evidenced by a localized sigma resonance, which broadens and shifts upward in energy when the lying-down chemisorbed molecules stand up. The localized chemisorption bond does not affect the electronic coupling between delocalized image resonances and the metal substrate. Instead, lifetimes of image resonances are decreased due to scattering with S atoms within the thiol or thiolate monolayer.     

Kinetics and mechanism for reduction of the anticancer prodrug trans,trans,trans-[PtCl2(OH)2(c-C6H11NH2)(NH3)] (JM335) by thiols

The reduction of the platinum(IV) prodrug trans,trans,trans-[PtCl2(OH)2(c-C6H11NH2)(NH3)] (JM335) by L-cysteine, DL-penicillamine, DL-homocysteine, N-acetyl-L-cysteine, 2-mercaptopropanoic acid, 2-mercaptosuccinic acid, and glutathione has been investigated at 25 degrees C in a 1.0 M aqueous perchlorate medium with 6.8 < or = pH < or = 11.2 using stopped-flow spectrophotometry. The stoichiometry of Pt(IV):thiol is 1:2, and the redox reactions follow the second-order rate law -d[Pt(IV)]/dt = k[Pt(IV)][RSH]tot, where k denotes the pH-dependent second-order rate constant and [RSH]tot the total concentration of thiol. The pH dependence of k is ascribed to parallel reductions of JM335 by the various protolytic species of the thiols, the relative contributions of which change with pH. Electron transfer from thiol (RSH) or thiolate (RS-) to JM335 is suggested to take place as a reductive elimination process through an attack by sulfur at one of the mutually trans chloride ligands, yielding trans-[Pt(OH)2(c-C6H11NH2)(NH3)] and RSSR as the reaction products, as confirmed by 1H NMR. Second-order rate constants for the reduction of JM335 by the various protolytic species of the thiols span more than 3 orders of magnitude. Reduction with RS- is approximately 30-2000 times faster than with RSH. The linear correlation log(kRS) = (0.52 +/- 0.06)-pKRSH--(2.8 +/- 0.5) is observed, where kRS denotes the second-order rate constant for reduction of JM335 by a particular thiolate RS- and KRSH is the acid dissociation constant for the corresponding thiol RSH. The slope of the linear correlation indicates that the reactivity of the various thiolate species is governed by their proton basicity, and no significant steric effects are observed. The half-life for reduction of JM335 by 6 mM glutathione (40-fold excess) at physiologically relevant conditions of 37 degrees C and pH 7.30 is 23 s. This implies that JM335, in clinical use, is likely to undergo in vivo reduction by intracellular reducing agents such as glutathione prior to binding to DNA. Reduction results in the immediate formation of a highly reactive platinum(II) species, i.e., the bishydroxo complex in rapid protolytic equilibrium with its aqua form.     

Synthesis and characterization of gold nanoparticles stabilized by palladium(II) phosphine thiol

This work is focused on the synthesis of innovative hybrids made by linking gold nanoparticles to protected organometallic Pd(II) thiolate. The organometallic protected Pd(II) thiolate, i.e. trans-thioacetate-ethynylphenyl-bis(tributylphosphine)palladium(II) has been synthesized, in situ deprotected and linked to Au nanoparticles. In this way new hybrid, with a direct link between Pd(II) and Au nanoparticles through a single S bridge, has been isolated. The combination of the organometallic Pd(II) thiol with gold nanoparticles allows the enhancement and tailoring of electronic and optical properties of the new organic-inorganic nano-compound. Single-crystal gold nanoparticles, uniform in shape and size were obtained by applying a modified two-phase method (improved Brust-Schiffrin reaction). In addition, the chemical environment of the Au nanoparticles was investigated and a covalent bonding between Au nanoparticles and the organometallic thiols was observed.     

Grafting of monocarboxylic substituted polychlorotriphenylmethyl radicals onto a COOH-functionalized self-assembled monolayer through copper (II) metal ions

A monocarboxylic substituted polychlorotriphenylmethyl radical (PTMCOOH) has been grafted onto a COOH-functionalized SAM (mercaptohexadecanoic acid, MHDA SAM), using copper (II) metal ions as linkers between the carboxyl groups of the SAM and the ligand. The metal-radical adlayer has been characterized thoroughly using different surface analysis techniques, such as contact angle, IRRAS, XPS, SPR, ToF-SIMS, SFM, and NEXAFS. The magnetic character was confirmed by EPR. The density of unoccupied states was investigated using X-ray absorption spectroscopy. A low-energy peak in the NEXAFS spectrum directly revealed the presence of partially occupied electronic levels, thus proving the open-shell character of the grafted ligands. SEM measurements on a laterally patterned sample prepared by muCP of MHDA in a matrix of hexadecane thiolate (a CH 3-terminated SAM) was performed to demonstrate that the metal-assisted anchoring of the open-shell ligand occurs selectively on the COOH terminated SAM. These results represent an easy and new approach to anchor organic radicals on surfaces and constitute a first step toward the growth of magnetic metal-organic radical-based frameworks on solid substrates.     

The Golden Pathway to Thiolate-Stabilized Nanoparticles: Following the Formation of Gold(I) Thiolate from Gold(III) Chloride

Pathways for the formation of gold thiolate complexes from gold(III) chloride precursors AuCl(4)(-) and AuCl(3) are examined. This work demonstrates that two distinct reaction pathways are possible; which pathway is accessible in a given reaction may depend on factors such as the residue group R on the incoming thiol. Density functional theory calculations using the BP86 functional and a polarized triple-ζ basis set show that the pathway resulting in gold(III) reduction is favored for R = methyl. A two-to-one ratio of thiol or thiolate to gold can reduce Au(III) to Au(I), and a three-to-one ratio can lead to polymeric Au(SR) species, which was first suggested by Schaaff et al. J. Phys. Chem. B, 1997, 101, 7885 and later confirmed by Goulet and Lennox J. Am. Chem. Soc., 2010, 132, 9582. Most transition states in the pathways examined here have reasonable barrier heights around 0.3 eV; we find two barrier heights that differ substantially from this which suggest the potential for kinetic control in the first step of thiolate-protected gold nanoparticle growth.     

Quantum chemistry studies of electronically excited nitrobenzene, TNA, and TNT

The electronic excitation energies and excited-state potential energy surfaces of nitrobenzene, 2,4,6-trinitroaniline (TNA), and 2,4,6-trinitrotoluene (TNT) are calculated using time-dependent density functional theory and multiconfigurational ab initio methods. We describe the geometrical and energetic character of excited-state minima, reaction coordinates, and nonadiabatic regions in these systems. In addition, the potential energy surfaces for the lowest two singlet (S(0) and S(1)) and lowest two triplet (T(1) and T(2)) electronic states are investigated, with particular emphasis on the S(1) relaxation pathway and the nonadiabatic region leading to radiationless decay of S(1) population. In nitrobenzene, relaxation on S(1) occurs by out-of-plane rotation and pyramidalization of the nitro group. Radiationless decay can take place through a nonadiabatic region, which, at the TD-DFT level, is characterized by near-degeneracy of three electronic states, namely, S(1), S(0), and T(2). Moreover, spin-orbit coupling constants for the S(0)/T(2) and S(1)/T(2) electronic state pairs were calculated to be as high as 60 cm(-1) in this region. Our results suggest that the S(1) population should quench primarily to the T(2) state. This finding is in support of recent experimental results and sheds light on the photochemistry of heavier nitroarenes. In TNT and TNA, the dominant pathway for relaxation on S(1) is through geometric distortions, similar to that found for nitrobenzene, of a single ortho-substituted NO(2). The two singlet and lowest two triplet electronic states are qualitatively similar to those of nitrobenzene along a minimal S(1) energy pathway.