烯烃分子在氢终止Si(100)-2×1表面的自由基链反应

应用密度泛函理论(DFT)和从头计算分子动力学方法(ab initio MD)研究了不饱和烯烃在氢终止的Si(100)-2×1表面的自由基链反应. 计算表明, 自由基链反应中重要的一步是烷烃链自由基的氢抽提过程, 硅表面上邻近位置(the nearest neighbor, NN)的氢抽提比次邻近位置(the next-nearest neighbor, NNN)的氢抽提有一稍低的能垒. 从头算分子动力学显示, 过渡态的烷烃自由基与氢终止Si(100)-2×1表面上的氢原子能够很容易形成C—H键, 完成一个氢抽提过程, 同时在硅表面产生下一个孤电子, 继续引发链反应.     

A DFT Study of Alkenes and Alkynes Reacting with H-GaN （0001） Surface

The addition reactions of alkenes and alkynes to the H-terminated GaN （0001） surface with a Ga dangling-bond have been studied employing periodic density functional theory （PDFT） calculations. Detailed information on the reaction pathways of these alkenes and alkynes with H-GaN （0001） surface is provided, which indicates that the reactions contain two steps separated by the metastable intermediates： elementary addition reaction and H-abstraction process. From the energy curves, the reactions are clearly viable in the cases of ethene, styrene and phenylacetylene; while for ethyne, the H-abstraction barrier is higher than the desorption barrier of the intermediate, so the adsorbed C2H2 in intermediate is more likely to be desorbed back into the gas phase than to form a stable adsorbed species. Furthermore, it is obvious that for either alkenes or alkynes, the systems substituted by phenyl have more stable intermediates because π conjugation could improve their stabilities.     

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).     

Self-directed growth of benzonitrile line on H-terminated Si(001) surface

Using first-principles density-functional calculations we predict a self-directed growth of benzonitrile molecular line on a H-terminated Si(001) surface. The C[triple bond]N bond of benzonitrile reacts with a single Si dangling bond which can be generated by the removal of a H atom, forming one Si-N bond and one C radical. Subsequently, the produced C radical can be stabilized by abstracting a H atom from a neighboring Si dimer, creating another H-empty site. This H-abstraction process whose activation barrier is 0.65 eV sets off a chain reaction to grow one-dimensional benzonitrile line along the Si dimer row. Our calculated energy profile for formation of the benzonitrile line shows its relatively easier formation compared with previously reported styrene and vinylferrocene lines.     

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.     

Dry synthesis of triple cumulative double bonds (C=C=C=N) on Si(111)-7 x 7 surfaces

The interactions of cyanoacetylene and diacetylene with a Si(111)-7 x 7 surface have been studied as model systems to mechanistically understand the chemical binding of unsaturated organic molecules to diradical-like silicon dangling bonds. Vibrational studies show that cyanoacetylene mainly binds to the surface through a diradical reaction involving both cyano and C[triple bond]C groups with an adjacent adatom-rest atom pair at 110 K, resulting in an intermediate containing triple cumulative double bonds (C=C=C=N). On the other hand, diacetylene was shown to the covalently attached to Si(111)-7 x 7 only through one of its C[triple bond]C groups, forming an enynic-like structure with a C=C-C[triple bond]C skeleton. These chemisorbed species containing triple cumulative double bonds (C=C=C=N) and C=C-C[triple bond]C may be employed as precursors (or templates) for further construction of bilayer organic films on the semiconductor surfaces.     

Diffusion by chemical bond hopping of single O2 and H on Si(111)-7×7 surfaces

Using a variable temperature STM to trace in detail the path of single particle movement, it is possible to derive diffusion parameters of individual atoms and molecules on solid surfaces as well as to probe the mechanisms. Below ˜370 °C, O₂ molecules adsorb on Si(111)-7×7 surfaces at the top site of Si-adatoms as bright image spots. An O₂ molecule can hop between two adatom sites within the half unit cell it adsorbs via two rest-atom sites. Above this temperature, it can either hop out of the half cell, or can go through other reaction pathways. In contrast, for H atoms, the adsorption sites are rest-atom sites. An H atom darkens the rest-atom in filled state image, but the surrounding adatoms will appear brighter because of a reverse charge transfer. Above ˜280 °C, it can hop to a neighbor rest atom site within the half cell via an adatom site. The adatom in the short lived intermediate state appears darker because of the saturation of its dangling bond. Above ˜340 °C, it can hop out of the half cell via two adatom sites. Thus diffusion of H and O₂ on this surface is achieved by hopping of chemical bonds via intermediate states. We have also derived site and pathway-specific activation energies and frequency factors and the potential energy curves for the hopping of O₂ and H on Si(111)-7×7 surfaces.     

Self-directed chain reaction by small ketones with the dangling bond site on the Si(100)-(2 x 1)-H surface: acetophenone, a unique example

Using scanning tunneling microscope (STM) at 300 K, we studied the growth of one-dimensional molecular assemblies (molecular lines) on the Si(100)-(2 x 1)-H surface through the chain reaction of small ketone (CH 3COCH 3, PhCOPh, and PhCOCH 3) molecules with dangling bond (DB) sites of the substrate. Acetone and benzophenone show the growth of molecular lines exclusively parallel to the dimer row direction. In contrast, acetophenone molecules show some molecular lines perpendicular, in addition to parallel, to the dimer row direction. Most of the molecular lines perpendicular to the dimer row direction were grown by self-turning the propagation direction of a chain reaction from parallel to perpendicular directions relative to the dimer row. A chiral center created upon adsorption of an acetophenone molecule allows the adsorbed molecules to align with identical as well as alternate enantiomeric forms along the dimer row direction, whereas such variations in molecular arrangement are not observed in the case of acetone and benzophenone molecules. The observed molecular lines growth both parallel and perpendicular to dimer row directions appears to be unique to acetophenone among all the molecules studied to date. Hence, the present study opens new possibility for fabricating one-dimensional molecular assemblies of various compositions in both high-symmetry directions on the Si(100)-(2 x 1)-H surface.     

Selective adsorption of pyridine at isolated reactive sites on Si(100)

Dative bonding of nitrogen-containing heterocycles offers a strategy for the controlled attachment of aromatic molecules to silicon surfaces. However, while scanning tunneling microscopy shows that pyridine on clean Si(100) initially binds via a dative bonding configuration, slow conversion to a more stable bridging state, destroying the aromaticity, is observed. To restrict adsorption to the dative bonded form, we investigated the interaction of pyridine with isolated reactive sites on partially H-terminated Si(100). While dative bonding on isolated clean dimers is observed, single dangling bonds remain unreacted. This selectivity can be accounted for by the ability of the Si-Si dimers to act as electron acceptors that stabilize the dative bonded species. This observation has important implications for the controlled positioning of single molecules on silicon via dative bonding.     

Reaction of alkyn-1-yl(diorganyl)silanes with 1-boraadamantane: Si-H-B bridges confirmed by the molecular structure in the solid state and in solution

1-Boraadamantane 1 was treated with alkyn-1-ylsilanes 2 containing one or two Si[bond]H functions. Under mild conditions, the reaction gave 4-methylene-3-borahomoadamantane derivatives 4 quantitatively and selectively by 1,1-organoboration. An electron deficient Si-H-B bridge was present in the product. The analogous reaction of 1 with an alkyn-1-yl-disilane 3 gave the corresponding alkene derivative 5, however, without the Si-H-B bridge. Evidence for the Si-H-B bridge in 4 was given by IR data, an extensive set of NMR spectroscopical data ((1)H, (11)B, (13)C, (29)Si NMR) including various unusual isotope effects on chemical shifts and coupling constants, as well as from the molecular structure of one example, 4 e, in the solid state. The precursor of 4 e, alkyne 2 e, Ph(2)Si(H)C[triple bond]CSi(H)Ph(2), was also studied by X-ray analysis.     

Mechanism insights of ethane C-H bond activations by bare [Fe(III)═O]+: explicit electronic structure analysis

Alkane C-H bond activation by various catalysts and enzymes has attracted considerable attention recently, but many issues are still unanswered. The conversion of ethane to ethanol and ethene by bare [Fe(III)═O](+) has been explored using density functional theory and coupled-cluster method comprehensively. Two possible reaction mechanisms are available for the entire reaction, the direct H-abstraction mechanism and the concerted mechanism. First, in the direct H-abstraction mechanism, a direct H-abstraction is encountered in the initial step, going through a collinear transition state C···H···O-Fe and then leading to the generation of an intermediate Fe-OH bound to the alkyl radical weakly. The final product of the direct H-abstraction mechanism is ethanol, which is produced by the hydroxyl group back transfer to the carbon radical. Second, in the concerted reaction mechanism, the H-abstraction process is characterized via overcoming four/five-centered transition states (6/4)TSH_c5 or (4)TSH_c4. The second step of the concerted mechanism can lead to either product ethanol or ethene. Moreover, the major product ethene can be obtained through two different pathways, the one-step pathway and the stepwise pathway. It is the first report that the former pathway starting from (6/4)IM_c to the product can be better described as a proton-coupled electron transfer (PCET). It plays an important role in the product ethene generation according to the CCSD(T) results. The spin-orbital coupling (SOC) calculations demonstrate that the title reaction should proceed via a two-state reactivity (TSR) pattern and that the spin-forbidden transition could slightly lower the rate-determining energy barrier height. This thorough theoretical study, especially the explicit electronic structure analysis, may provide important clues for understanding and studying the C-H bond activation promoted by iron-based artificial catalysts.     

Isolation of an Eleven‐Atom Polydentate Carbon‐Chain Chelate Obtained by Cycloaddition of a Cyclic Osmium Carbyne with an Alkyne

Carbon ligands have long played an important role in organometallic chemistry. However, previous examples of all‐carbon chelating ligands are limited. Herein, we present a novel complex with an eleven‐atom carbon chain as a polydentate chelating ligand. This species was formed by the [2+2+2] cycloaddition reaction of two equivalents of an alkyne with an osmapentalyne that contains the smallest carbyne bond angle (127.9°) ever observed. Density functional calculations revealed that electron‐donating groups play a key role in the stabilization of this polydentate carbon‐chain chelate. This process is also the first [2+2+2] cycloaddition reaction of an alkyne with a late‐transition‐metal carbyne complex. This study not only enriches the chemistry of polydentate carbon‐chain chelates, but also deepens our understanding of the chelating ability of carbon ligands.     

Competing forward and reversed chain reactions in one-dimensional molecular line growth on the Si(100)-(2 x 1)-H surface

To explore the role of competing forward and reversed chain reactions in the growth of a one-dimensional (1D) molecular line on the Si(100)-(2 x 1)-H surface, controlled experiments were performed with various alkene molecules by scanning tunneling microscopy (STM) at various temperatures. It was observed that the end dangling bond (DB) of a styrene line, fabricated by a chain reaction on the Si(100)-(2 x 1)-H surface at 300 K, initiated a reverse chain reaction at 400 K, leading to the complete disappearance of the styrene line with zero-order desorption kinetics (rate constant k = 1.17 x 10-2 s-1 at 400 K). In the case of 2,4-dimethylstyrene, the reversed chain reaction was observed even at 300 K. These results suggest that the appearance of a molecular line in an STM image is determined by the rates of competing forward and reversed chain reactions at a given temperature. As predicted, 1D lines formed by the DB-initiated chain reaction of 1-hexene and 1-heptene on Si(100)-(2 x 1)-H were observed at 180 K because of the reduced desorption rate, despite the fact that those molecules showed no line growth at 300 K. These results indicate that the scope of forming 1D molecular lines on the Si(100)-(2 x 1)-H surface with various alkenes is much wider than anticipated in previous studies.     

Cyclopropenylmethyl Cation: A Concealed Intermediate in Gold(I)‐Catalyzed Reactions

The last years have witnessed many gold‐catalyzed reactions of alkynes. One of the most prominent species in the reaction of two alkyne units is the vinyl‐substituted gold vinylidene intermediate. Here, we were able to show that the reaction of a haloacetylene and an alkyne proceeds via a hitherto overlooked intermediate, namely the cyclopropenylmethyl cation. The existence and relative stability of this concealed intermediate is verified by quantum chemical calculations and ¹³C‐labeling experiments. A comparison between the cyclopropenylmethyl cation and the well‐known vinylidene intermediate reveals that the latter is more stable only for smaller cycles. However, this stability reverses in larger cycles. In the case of the smallest representative of both species, the vinylidene cation is the transition state en route to the cyclopropenylmethyl cation. The discovery of this intermediate should help to get a deeper understanding for gold‐catalyzed carbon–carbon bond‐forming reactions of alkynes. Furthermore, since enynes can be formed from the cyclopropenylmethyl cation, the inclusion of this intermediate should enable the development of new synthetic methods for the construction of larger cyclic halogenated and non‐halogenated conjugated enyne systems.     

SiCNN--a new stable isomer with Si(triple bond)C triple bonding

To predict potentially stable molecules with Si(triple bond)C triple bonding, theoretical calculations at the B3LYP/ 6-311G(d) and CCSD(T)/6-311G(2df) (single-point) levels were employed to study the structures, energetics, and isomerization of various SiCN2 isomers. A schematic potential energy surface (PES) of SiCN2 was established to discuss the kinetic stability of the isomers. A new isomer SiCNN was found to possess a typical Si(triple bond)C triple bond, as confirmed by comparative calculations at the B3LYP, QCISD, QCISD(T), CCSD, and CCSD(T) levels on the bond lengths of SiCNN and other experimentally or theoretically known species of RSiCH (R = H, F, Cl, OH). Moreover, SiCNN resides in a very deep potential, the stabilization barrier is at least 53.2 kcal mol(-1). Thus, SiCNN may be considered as the most kinetically stable isomer with Si(triple bond)C triple bonding known to date, and it may represent a very promising molecule for future experimental characterization. In addition, the stability of the other isomers, such as the four linear species SiNCN, SiNNC, NSiCN and NSiNC, a three-membered NNC ring isomer with exocyclic C-Si bonding, and a four-membered SiCNN ring isomer is discussed and compared with SiCNN.     

X-ray studies of self-assembled organic monolayers grown on hydrogen-terminated Si(111)

The structure of self-assembled monolayers (SAMs) of undecylenic acid methyl ester (SAM-1) and undec-10-enoic acid 2-bromo-ethyl ester (SAM-2) grown on hydrogen-passivated Si(111) were studied by X-ray reflectivity (XRR), X-ray standing waves (XSW), X-ray fluorescence (XRF), atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). The two different SAMs were grown by immersion of H-Si(111) substrates into the two different concentrated esters. UV irradiation during immersion was used to create Si dangling bond sites that act as initiators of the surface free-radical addition process that leads to film growth. The XRR structural analysis reveals that the molecules of SAM-1 and SAM-2 respectively have area densities corresponding to 50% and 57% of the density of Si(111) surface dangling bonds and produce films with less than 4 angstroms root-mean-square roughness that have layer thicknesses of 12.2 and 13.2 angstroms. Considering the molecular lengths, these thicknesses correspond to a 38 degrees and 23 degrees tilt angle for the respective molecules. For SAM-2/Si(111) samples, XRF analysis reveals a 0.58 monolayer (ML) Br total coverage. Single-crystal Bragg diffraction XSW analysis reveals (unexpectedly) that 0.48 ML of these Br atoms are at a Si(111) lattice position height that is identical to the T1 site that was previously found by XSW analysis for Br adsorbed onto Si(111) from a methanol solution and from ultrahigh vacuum. From the combined XPS, XRR, XRF, and XSW evidence, it is concluded that Br abstraction by reactive surface dangling bonds competes with olefin addition to the surface.     

Formation of organic monolayers on silicon via gas-phase photochemical reactions

A new method for the formation of molecular monolayers on silicon surfaces utilizing gas-phase photochemical reactions is reported. Hydrogen-terminated Si(111) surfaces were exposed to various gas-phase molecules (hexene, benzaldehyde, and allylamine) and irradiated with ultraviolet light from a mercury lamp. The surfaces were studied with in situ Fourier transform infrared spectroscopy, high-resolution electron energy loss spectroscopy, and scanning tunneling microscopy. The generation of gas-phase radicals was found to be the initiator for organic monolayer formation via the abstraction of hydrogen from the H/Si(111) surface. Monolayer growth can occur through either a radical chain reaction mechanism or through direct radical attachment to the silicon dangling bonds.     

Protection-deprotection chemistry to control styrene self-directed line growth on hydrogen-terminated Si(100)

TEMPO, 2,2,6,6-tetramethylpiperidinyloxy, was used in a series of protection-deprotection chemical reactions in order to gain single molecule-level control over the extent of styrene line growth on hydrogen-terminated Si(100). The mechanism involves the reaction of TEMPO with the dangling bond at the end of individual styrene lines. The TEMPO cap protects the dangling bond from further reaction with styrene resulting in the termination of line growth. TEMPO is then selectively removed from desired lines, deprotecting the dangling bond, using the scanning tunneling microscope. Further exposure of the surface to styrene ensures that only the deprotected areas continue to grow while the protected lines do not. All lines can then be capped with TEMPO, and this allows for the generation of stable styrene lines of varying lengths.     

Theoretical study of oxidation of cyclohexane diol to adipic anhydride by [Ru(IV)(O)(tpa)(H2O)]2+ complex (tpa ═ tris(2-pyridylmethyl)amine)

The catalytic conversion of 1,2-cyclohexanediol to adipic anhydride by Ru(IV)O(tpa) (tpa ═ tris(2-pyridylmethyl)amine) is discussed using density functional theory calculations. The whole reaction is divided into three steps: (1) formation of α-hydroxy cyclohexanone by dehydrogenation of cyclohexanediol, (2) formation of 1,2-cyclohexanedione by dehydrogenation of α-hydroxy cyclohexanone, and (3) formation of adipic anhydride by oxygenation of cyclohexanedione. In each step the two-electron oxidation is performed by Ru(IV)O(tpa) active species, which is reduced to bis-aqua Ru(II)(tpa) complex. The Ru(II) complex is reactivated using Ce(IV) and water as an oxygen source. There are two different pathways of the first two steps of the conversion depending on whether the direct H-atom abstraction occurs on a C-H bond or on its adjacent oxygen O-H. In the first step, the C-H (O-H) bond dissociation occurs in TS1 (TS2-1) with an activation barrier of 21.4 (21.6) kcal/mol, which is followed by abstraction of another hydrogen with the spin transition in both pathways. The second process also bifurcates into two reaction pathways. TS3 (TS4-1) is leading to dissociation of the C-H (O-H) bond, and the activation barrier of TS3 (TS4-1) is 20.2 (20.7) kcal/mol. In the third step, oxo ligand attack on the carbonyl carbon and hydrogen migration from the water ligand occur via TS5 with an activation barrier of 17.4 kcal/mol leading to a stable tetrahedral intermediate in a triplet state. However, the slightly higher energy singlet state of this tetrahedral intermediate is unstable; therefore, a spin crossover spontaneously transforms the tetrahedral intermediate into a dione complex by a hydrogen rebound and a C-C bond cleavage. Kinetic isotope effects (k(H)/k(D)) for the electronic processes of the C-H bond dissociations calculated to be 4.9-7.4 at 300 K are in good agreement with experiment values of 2.8-9.0.