Nanografting: modeling and simulation

We present a simple phenomenological model of the nanografting process with an emphasis on the formation of binary self-assembled monolayers. This model includes dynamical processes that are involved in natural growth experiments, including molecular deposition, surface diffusion, and the phase transition from physisorption to chemisorption, and we show that it predicts domain formation in ungrafted deposition that matches experiment. The one-order-of-magnitude faster kinetics that is found in the nanografting experiments compared to natural self-assembly (or unconstrained self-assembly) is described with a key assumption that the deposition rate is greatly enhanced in the small region confined between the back side of the AFM tip and the edge of the previously deposited self-assembled monolayer. Monte Carlo simulations based on this model reproduce experimental observations concerning the variation of SAM heterogeneity with AFM tip speed. Our simulations demonstrate that the faster the AFM tip displaces adsorbed molecules in a monolayer, the more heterogeneous are the monolayers formed behind the tip, as this allows space and time for the formation of phase-segregated domains.     

Role of molecular conjugation in the surface radical reaction of aldehydes with H-Si(111): first principles study

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).     

Linear nanostructure formation of aldehydes by self-directed growth on hydrogen-terminated silicon(100)

The self-directed growth of organic molecules on silicon surfaces allows for the rapid, parallel production of hybrid organic-silicon nanostructures. In this work, the formation of benzaldehyde- and acetaldehyde-derived nanostructures on hydrogen-terminated H-Si(100)-2x1 surface is studied by scanning tunneling microscopy in ultrahigh vacuum and by quantum mechanical methods. The reaction is a radical-mediated process that binds the aldehydes, through a strong Si-O covalent bond, to the surface. The aldehyde nanostructures are generally composed of double lines of molecules. Two mechanisms that lead to double line growth are elucidated.     

Density functional theory study of one-dimensional growth of styrene on the hydrogen-terminated Si(001)-(3 x 1) surface

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.     

Infrared spectroscopic investigation of the reaction of hydrogen-terminated, (111)-oriented, silicon surfaces with liquid methanol

Fourier transform infrared spectroscopy and first principles calculations have been used to investigate the reaction of atomically smooth, hydrogen-terminated Si(111) (H-Si) surfaces with anhydrous liquid methanol. After 10 min of reaction at room temperature, a sharp absorbance feature was apparent at approximately 1080 cm(-1) that was polarized normal to the surface plane. Previous reports have identified this mode as a Si-O-C stretch; however, the first principles calculations, presented in this work, indicate that this mode is a combination of an O-C stretch with a CH3 rock. At longer reaction times, the intensity of the Si-H stretching mode decreased, while peaks attributable to the O-C coupled stretch and the CH3 stretching modes, respectively, increased in intensity. Spectra of H-Si(111) surfaces that had reacted with CD3OD showed the appearance of Si-D signals polarized normal to the surface as well as the appearance of vibrations indicative of Si-OCD3 surface species. The data are consistent with two surface reactions occurring in parallel, involving (a) chemical attack of hydrogen-terminated Si(111) terraces by CH3OH, forming Si-OCH3 moieties having their Si-O bond oriented normal to the Si(111) surface and (b) transfer of the acidic hydrogen of the methanol to the silicon surface, either through a direct H-to-D exchange mechanism or through a mechanism involving chemical step-flow etching of Si-H step sites.     

Formation of uniform ferrocenyl-terminated monolayer covalently bonded to Si using reaction of hydrogen-terminated Si(111) surface with vinylferrocene/n-decane solution by visible-light excitation

Electrochemically active self-assembled monolayers (SAM) have been successfully fabricated with atomic-scale uniformity on a silicon (Si)(111) surface by immobilizing vinylferrocene (VFC) molecules through Si-C covalent bonds. The reaction of VFC with the hydrogen-terminated Si (H-Si)(111) surface was photochemically promoted by irradiation of visible light on a H-Si(111) substrate immersed in n-decane solution of VFC. We found that aggregation and polymerization of VFC was avoided when n-decane was used as a solvent. Voltammetric quantification revealed that the surface density of ferrocenyl groups was 1.4×10(-10) mol cm(-2), i.e., 11% in substitution rate of Si-H bond. VFC-SAMs were then formed by the optimized preparation method on n-type and p-type Si wafers. VFC-SAM on n-type Si showed positive photo-responsivity, while VFC-SAM on p-type Si showed negative photo-responsivity.     

Comparative study on reactions and self-directed growth mechanisms of styrene molecules on H-terminated Si(111) and Si(100): combining quantum chemistry and molecular mechanics simulations

A comparative study on mechanisms of radical initiated self-directed growth of styrene molecules on the H-terminated Si(111) and Si(100) has been carried out by using quantum chemical and molecular mechanics methods. Several possible H-abstraction pathways through formations of transition states containing five-, six-, and even eight-membered ring structures are investigated with the aid of surface cluster models and density functional theory calculations. It has been demonstrated by employing periodic surface models and molecular mechanics simulations that the surface pattern and intermolecular interactions between phenyl groups play important roles in the self-directed growth processes. The formation of cluster-shaped aggregation of styrene molecules on H-Si(111) results from the undirectional chain reactions, due to the isotropic hexagonal arrangement of surface sites. On the contrary, the anisotropic style of H-Si(100) induces a strong directional preference for H-abstractions, following an order of the inter Si-Si dimer > the intra Si-Si dimer > the inter Si-Si dimer row. The one-dimensionally ordered structures of single and double lines along the Si-Si dimer row are thus formed on H-Si(100). The self-directed growths of styrene molecules on both H-Si(111) and H-Si(100) are revealed to be stage-dependent.     

Chemical reaction of nitric oxides with the 5-1DB defect of the single-walled carbon nanotube

In this work, we applied a two-layered ONIOM (B3LYP/6-31G(d):UFF) method to study the reaction of nitric oxides with a 5-1DB defect on the sidewall of the single-walled carbon nanotube (SWCNT). We have chosen a suitable ONIOM model for the calculation of the SWCNT based on the analyses of the frontier molecular orbitals, local density of states, and natural bond orbitals. Our calculations clearly indicate that the 5-1DB defect is the chemically active center of the SWCNT. In the reaction of nitric oxides with the defected SWCNT, the 5-1DB defect site can capture a nitrogen atom from nitric oxides, yielding the N-substitutionally doped SWCNT. We have explored the reaction pathway in detail. Our work verifies the chemical reactivity of the 5-1DB defects of the SWCNTs, indicates that the 5-1DB defect is a possible site for the functionalization of the SWCNTs, and demonstrates a possible way to fabricate position controllable substitutionally doped SWCNTs with a low doping concentration under mild conditions via some simple chemical reactions.     

Mechanistic Insights into the Substrate‐Controlled Stereochemistry of Glycals in One‐Pot Rhodium‐Catalyzed Aziridination and Aziridine Ring Opening

We carried out a principle study on the reaction mechanism of rhodium‐catalyzed intramolecular aziridination and aziridine ring opening at a sugar template. A sulfamate ester group was introduced at different positions of glycal to act as a nitrene source and, moreover, to allow the study of the relative reactivity of the nitrene transfer from different sites of the glycal molecule. The structural optimization of each intermediate along the reaction pathway was extensively done by using BPW91 functional. The crucial step in the reaction is the Rh‐catalyzed nitrene transfer to the double bond of the glycal. We found that the reaction could proceed in a stepwise manner, whereby the N atom initially induced a single‐bond formation with C1 on the triplet surface or in a single step through intersystem crossing (ISC) of the triplet excited state of the rhodium–nitrene transition state to the singlet ground state of the aziridine complexes. The relative reactivity for the conversion of the nitrene species to the aziridine obtained from the computed potential energy surface (PES) agrees well with the reaction time gained from experimental observation. The aziridine ring opening is a spontaneous process because the energy barrier for the formation of the transition state is very small and disappears in the solution calculations. The regio‐ and stereoselectivity of the reaction product is controlled by the electronic property of the anomeric carbon as well as the facial preference for the nitrene insertion, and the nucleophilic addition.     

Adsorption of 3-pyrroline on Si(100) from first principles

The chemisorption of 3-pyrroline (C(4)H(7)N) on Si(100) is studied from first principles. Three different structures can be realized for which, depending on the temperature, the chemisorption process is facile (for two of them it is essentially barrierless); among these configurations the most favored one, from a thermodynamical point of view, is a dissociated structure obtained through an exothermic reaction characterized by the formation of a N-Si bond and a H-Si bond in which the H atom is detached from the molecule. Several other chemisorption structures are possible which, however, require overcoming a significant energy barrier and often breaking multiple bonds. A number of reaction paths going from one stable structure to another have been investigated. We have also generated, for the two basic adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements, and we propose a possible reaction mechanism for nitrogen incorporation.     

Immobilization of ligands with precise control of density to electroactive surfaces

We report a broadly applicable surface chemistry methodology to immobilize ligands, proteins, and cells to an electroactive substrate with precise control of ligand density. This strategy is based on the coupling of soluble aminooxy terminated ligands with an electroactive quinone terminated monolayer. The surface chemistry product oxime is also redox active but at a different potential and therefore allows for real-time monitoring of the immobilization reaction. Only the quinone form of the immobilized redox pair is reactive with soluble aminooxy groups, which allows for the determination of the yield of reaction, the ability to immobilize multiple ligands at controlled densities, and the in-situ modulation of ligand activity. We demonstrate this methodology by using cyclic voltammetry to characterize the kinetics of a model interfacial reaction with aminooxy acetic acid. We also demonstrate the synthetic flexibility and utility of this method for biospecific interactions by installing aminooxy terminated FLAG peptides and characterizing their binding to soluble anti-FLAG with surface plasmon resonance spectroscopy. We further show this methodology is compatible with microarray technology by printing rhodamine-oxyamine in various size spots and characterizing the yield within the spots by cyclic voltammetry. We also show this methodology is compatible with cell culture conditions and fluorescent microscopy technology for cell biological studies. Arraying RGD-oxyamine peptides on these substrates allows for bio-specific adhesion of Swiss 3T3 Fibroblasts.     

Modulation of fragmental charge transfer via hydrogen bonds. Direct measurement of electronic contributions

Hydrogen bonds play an important role in an overwhelming variety of fields from biology to surface and supramolecular chemistry. The term "hydrogen bond" refers to a wide range of interactions with various covalent and polar contributions. In particular, hydrogen bonds have an important role in the folding and packing of peptides and nucleic acids. Recent studies also point to the importance of hydrogen bonding in the context of second-shell interactions, in metal binding and selectivity in metalloproteins, and in controlling the dynamics of membrane proteins. In this study, we demonstrate and quantify the modulation of fragmental charge transfer from hydrogen-bonded ligands to a metal center, by employing our recently introduced molecular potentiometer. The molecular details that affect this type of fragmental charge transfer are presented and a path for transferring chemical information is demonstrated. We found that H-bond interactions in the extended positions of axial ligands provide an effective means of modulating the amount of fragmental charge transfer to a metal center, thereby dramatically influencing the electronic properties of the ligand, the binding affinity, and the binding of additional ligands. The magnitude of fragmental charge-transfer modulation induced by a single ligand-solvent H-bond interaction is comparable to those induced by covalent substitution, although H-bond enthalpy is only on the order of several kilojoules per mole. Importantly, we find a significant change in the ligand electronic properties, even for weak C-H...O=C H-bond formation, where the bond enthalpy is substantially lower than for conventional H-bond interactions. The excess fragmental charge transferred to the metal center, deduced from the spectroscopic measurements, correlates well with the computationally determined values. Our findings underscore the importance of second-shell interactions in the active sites of enzymes, beyond the structural and electrostatic importance that is widely recognized today.     

Fabrication of interconnected 1D molecular lines along and across the dimer rows on the Si(100)-(2 x 1)-H surface through the radical chain reaction

To realize nanoscale wiring in two dimensions (2D), the fabrication of interconnected one-dimensional (1D) molecular lines through the radical chain reaction of alkene molecules (CH2=CH-R) on the H-terminated Si(100)-(2 x 1) surface have been investigated using scanning tunneling microscopy (STM) at 300 K. By the judicious choice of R in the CH2=CH-R molecule and by creating a dangling bond (DB) at a desired point using the STM tip, the perpendicularly connected allyl mercaptan (ALM) and styrene lines have been fabricated on the Si(100)-(2 x 1)-H surface. The continuous growth of the styrene line at the end DB of a growing ALM line (or vice versa) does not occur, perhaps, due to steric hindrance or/and interaction between adsorbed molecules.     

A Single‐Molecule‐Level Mechanistic Study of Pd‐Catalyzed and Cu‐Catalyzed Homocoupling of Aryl Bromide on an Au(111) Surface

On‐surface Pd‐ and Cu‐catalyzed C?C coupling reactions between phenyl bromide functionalized porphyrin derivatives on an Au(111) surface have been investigated under ultra‐high vacuum conditions by using scanning tunneling microscopy and kinetic Monte Carlo simulations. We monitored the isothermal reaction kinetics by allowing the reaction to proceed at different temperatures. We discovered that the reactions catalyzed by Pd or Cu can be described as a two‐phase process that involves an initial activation followed by C?C bond formation. However, the distinctive reaction kinetics and the C?C bond‐formation yield associated with the two catalysts account for the different reaction mechanisms: the initial activation phase is the rate‐limiting step for the Cu‐catalyzed reaction at all temperatures tested, whereas the later phase of C?C formation is the rate‐limiting step for the Pd‐catalyzed reaction at high temperature. Analysis of rate constants of the Pd‐catalyzed reactions allowed us to determine its activation energy as (0.41±0.03) eV.     

Controlled self-assembly of hydrophobic quantum dots through silanization

We demonstrate the formation of one-, two-, and three-dimensional nanocomposites through the self-assembly of silanized CdSe/ZnS quantum dots (QDs) by using a controlled sol-gel process. The self-assembly behavior of the QDs was created when partially hydrolyzed silicon alkoxide monomers replaced hydrophobic ligands on the QDs. We examined systematically self-assembly conditions such as solvent components and QD sizes in order to elucidate the formation mechanism of various QD nanocomposites. The QD nanocomposites were assembled in water phase or on the interface of water and oil phase in emulsions. The partially hydrolyzed silicon alkoxides act as intermolecules to assemble the QDs. The QD nanocomposites with well-defined solid or hollow spherical, fiber-like, sheet-like, and pearl-like morphologies were prepared by adjusting the experimental conditions. The high photoluminescence efficiency of the prepared QD nanocomposites suggests partially hydrolyzed silicon alkoxides reduced the surface deterioration of QDs during self-assembly. These techniques are applicable to other hydrophobic QDs for fabricating complex QD nanocomposites.     

Advances in understanding the role of surface hole formation in heterogeneous water oxidation

The electrochemical oxidation of water to molecular oxygen, that is, the oxygen evolution reaction (OER), is a key anodic reaction that supplies electrons and protons for many technologically interesting reduction processes, such as carbon dioxide reduction and nitrogen fixation. Because the OER is a slow reaction, it needs to be facilitated by (photo)electrocatalysts. To develop such catalysts, advances in the mechanistic understanding of the OER are critical. In this opinion, we focus on a key aspect of the OER, namely, how the accumulation of oxidative charge (‘holes’) on the surface of a catalyst triggers O ? O bond formation. We discuss recent advances in understanding the factors that drive surface hole formation at specific sites.     

Theoretical prediction of heterogeneous molecular wires on the Si(001) surface

Using first-principles density-functional calculations, we propose a self-assembly technique for fabrication of the heterogeneous molecular wire on the dangling-bond wire generated on a H-passivated Si(001) surface. Here, we choose pyridine and borine as Lewis base and acid molecules, respectively, to demonstrate different behaviors in the chemical reactivity and selectivity on the dangling-bond wire, leading to formation of the heterogeneous pyridine-borine wire.     

Comparison of various coupling reagents in solid-phase aza-peptide synthesis

Aza-peptides are promising drug leads, however extensive study of their properties is hampered by low yielding aza-peptide bond formation during conventional Fmoc SPPS. The kinetics of aza-peptide bond formation in the model peptide H-Ala-AzAla-Phe-NH₂ was compared with various conventional amino acid activators. The reaction rates and yields were dependent on the activator structure. The reaction time of aza-peptide formation using oxyma-based agents was approximately 30 times longer than in typical peptide synthesis. Therefore, new activators are required to increase the reactivity of the activated amino acid to achieve effective acylation of the semicarbazide moiety during aza-peptide bond formation.     

Role of water in atomic resolution AFM in solutions

We use computer modelling to investigate the mechanism of atomic-scale corrugation in frequency modulation atomic force microscopy imaging of inorganic surfaces in solution. Molecular dynamics simulations demonstrate that the forces acting on a model microscope tip result from the direct interaction between a tip and a surface, and forces entirely due to the water structure around both tip and surface. The observed force is a balance between largely repulsive potential energy changes as the tip approaches and the entropic gain when water is sterically prevented from occupying sites near the tip and surface. Only extremely sharp tips are likely to measure direct tip-surface interactions. An investigation into the dynamics of water confined between tip and surface shows that water diffusion can be slowed by at least two orders of magnitude compared to its rate in bulk solution.     

Controlling Single Molecule Conductance by a Locally Induced Chemical Reaction on Individual Thiophene Units

Among the prerequisites for the progress of single‐molecule‐based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ‐induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.