Self-induced 1-D molecular chain growth of thiophene on Ge(100)

The adsorption of thiophene on Ge(100) has been studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculations. Until now, thiophene is known to react with the Ge(100) dimer through a [4 + 2] cycloaddition reaction at room temperature, similar to the case of thiophene on Si(100). However, we found that thiophene has two adsorption geometries on Ge(100) at room temperature, such as a kinetically favorable Ge-S dative bonding configuration and a thermodynamically stable [4 + 2] cycloaddition adduct. Moreover, our STM results show that under 0.25 ML thiophene molecules preferentially produce one-dimensional molecular chain structures on Ge(100) via the Ge-S dative bonding configuration.     

Surface chemistry of five-membered aromatic ring molecules containing two different heteroatoms on Si(111)-7 x 7

The surface chemistry of three representative aromatic molecules containing two different heteroatoms isoxazole, oxazole, and thiazole on Si(111)-7 x 7 was studied. These molecules exhibit different competition and selectivity for multiple reaction channels with this surface, determined by a combination of molecular electronic and structural factors. Isoxazole is chemically attached to Si(111)-7 x 7 through both dative-bond addition and [4 + 2]-like cycloaddition. Oxazole chemisorbs on Si(111)-7 x 7 through both dative-bond addition and [2 + 2]-like cycloaddition. The kinetically favored [2 + 2]-like cycloadduct at low temperature is thermally converted into the thermodynamically preferred [4 + 2]-like cycloadduct at a temperature higher than 300 K. Thiazole is chemically bound to this surface only through formation of a Si...N dative bond at low temperature. This dative-bonded molecule is thermally converted into a [4 + 2]-like cycloadduct. The reaction channels of the three five-membered aromatic molecules containing two different heteroatoms (isoxazole, oxazole, and thiazole) and of the aromatic molecules containing only one heteroatom (pyridine, pyrrole, furan, and thiophene) are compared and analyzed for a thorough understanding of the reaction mechanisms of various heterocyclic aromatic molecules on this surface. The intrinsic connection between surface reaction mechanism and molecular electronic structure is demonstrated. This includes the distribution of electron density on the molecular ring determined by the geometric arrangement of the heteroatoms, the electronegativity of the heteroatoms, and the electronic contribution of the heteroatoms to formation of aromatic pi conjugation, as well as the molecular polarity.     

Competition and selectivity of organic reactions on semiconductor surfaces: reaction of unsaturated ketones on Si(100)-2 x 1 and Ge(100)-2 x 1

A combined experimental and theoretical study of a model system of multifunctional unsaturated ketones, including ethyl vinyl ketone (EVK), 2-cyclohexen-1-one, and 5-hexen-2-one, on the Si(100)-2 x 1 and Ge(100)-2 x 1 surfaces was performed in order to probe the factors controlling the competition and selectivity of organic reactions on clean semiconductor surfaces. Multiple internal reflection infrared spectroscopy data and density functional theory calculations indicate that EVK and 2-cyclohexen-1-one undergo selective [4 + 2] hetero-Diels-Alder and [4 + 2] trans cycloaddition reactions on the Ge(100)-2 x 1 surface at room temperature. In contrast, on the Si(100)-2 x 1 surface, evidence is seen for significant ene and possibly [2 + 2] C=O cycloaddition side products. The greater selectivity of these compounds on Ge(100) versus Si(100) is explained by differences between the two surfaces in both thermodynamic factors and kinetic factors. With 5-hexen-2-one, for which [4 + 2] cycloaddition is not possible, a small [2 + 2] C=C cycloaddition product is observed on Ge(100) and possibly Si(100), even though the [2 + 2] C=C transition state is calculated to be the highest barrier reaction by several kilocalories per mole. The results suggest that, due to the high reactivity of clean semiconductor surfaces, thermodynamic selectivity and control will play important roles in their selective functionalization, favoring the use of Ge for selective attachment of multifunctional organics.     

Reaction Behaviors of S-, O-, and N-containing Aliphatic Molecules with a Propyl Moiety on Ge(100) Surface

The reaction pathways of 1-propanethiol, 1-propanol, and propylamine molecules, containing a propyl moiety, on a Ge(100) surface were investigated using high-resolution photoemission spectroscopy (HRPES) experiments and density functional theory (DFT) calculations. Upon analysis of the HRPES data, the adsorption of 1-propanethiol and 1-propanol was found to occur through a dissociation reaction, whereas that of propylamine took place via N dative bonding at room temperature. On the basis of our DFT results, adsorption geometries and transition states for each of these molecules on the Ge(100) surface were confirmed. Systematic studies of S-, O-, and N-containing molecules, composed of an identical propyl moiety, on the Ge(100) surface provide insight into the adsorption mechanism of aliphatic molecules containing alkyl chains on the Ge(100) surface.     

Adsorption mechanisms of isoxazole and oxazole on Si(100)-2 × 1 surface: Si-N dative bond addition vs. [4+2] cycloaddition

The surface reaction pathways of isoxazole and oxazole on Si(100)-2 × 1 surface were theoretically investigated. They both form a weakly bound Si-N dative bond adduct on Si(100)-2 × 1 surface. In the case of isoxazole, the barrierlessly formed Si-N adduct is the most important surface product, that cannot be easily converted into other species. On the other hand, a facile concerted [4+2](CC) cycloaddition without involving the initial Si-N dative bond adduct was also found in the case of oxazole adsorption. The existence of Diels-Alder reactions is attributed to the particular arrangement of the two heteroatoms of oxazole in such a way that the two Si-C σ-bonds can be formed in a [4+2] fashion. In short, the unique geometric arrangements and electronegativity of these similar heteroatomic molecules yielded distinctively different surface reaction characteristics.     

Coverage‐Dependent Variation of Adsorption Configurations of Methionine on Ge(100)

The adsorption configurations of methionine molecules on the Ge(100) surface have been studied by using DFT calculations, core‐level photoemission spectroscopy (CLPES), and low‐energy electron diffraction (LEED) to scrutinize the adsorption structure as a function of coverage. At first, we obtained two important and stable structures. One is the most stable structure between these structures described as an “O H dissociated‐N dative‐S dative‐bonded structure” and the other is a less stable adsorption structure of these indicating an “O H dissociated‐S dative‐bonded structure” by using DFT calculations. We also performed CLPES to clarify our DFT calculation results. Through the spectral analysis of the S 2p, C 1s, N 1s, and O 1s core‐level spectra, we acquired the reasonable results that also revealed quite different bonding configurations depending on the methionine coverage. At low coverage (ca. 0.30 ML), a single type of sulfur and charged nitrogen peaks, which indicate an “O H dissociated‐N dative‐S dative‐bonded structure”, were observed. On the other hand, two types of sulfur peaks with thiol formation and two nitrogen peaks with neutralized and charged characteristics were monitored at a higher coverage (0.60 ML and above), which can be described as an “O H dissociated‐S dative‐bonded structure”. Hence, we can clearly demonstrate that our results obtained from CLPES spectra and DFT calculations are matched well with each other. Moreover, we additionally confirmed that the relative population of the two types of thiols and amines being included in methionine in between half monolayer induces a surface reorientation in the ordering from 2×1 to 1×1 employing LEED. This interesting variation of the methionine adsorbed on the Ge(100) surface by coverage dependence will be precisely discussed by using DFT calculations, CLPES, and LEED.     

Formation of highly ordered organic monolayers by dative bonding: pyridine on ge(100)

The adsorption of pyridine onto the Ge(100) surface has been studied using both real-time scanning tunneling microscopy (STM) and ab initio pseudopotential density functional calculations. The results show that pyridine molecules adsorb on the electron-deficient down-Ge atoms of the Ge=Ge dimers via Ge-N dative bonding, with the pyridine ring tilted to the surface. The electron-rich up-Ge atoms remaining after adsorption of pyridine induce an asymmetric dimer row, which is mainly reconstructed to the c(4 x 2) structure. At pyridine coverage of 0.25 ML, the adsorbed pyridine molecules form a perfectly ordered monolayer. The entire Ge substrate underlying this organic monolayer rearranges into the c(4 x 2) structure.     

Diradical mechanisms for the cycloaddition reactions of 1,3-butadiene,benzene, thiophene,ethylene, and acetylene on a Si(111)-7x7 surface

The cycloaddition chemistry of several representative unsaturated hydrocarbons (1,3-butadiene, benzene, ethylene, and acetylene) and a heterocyclic aromatic (thiophene) on a Si(111)-7x7 surface has been explored by means of density functional cluster model calculations. It is shown that (i) 1,3-butadiene, benzene, and thiophene can undergo both [4+2]-like and [2+2]-like cycloadditions onto a rest atom-adatom pair, with the former process being favored over the latter both thermodynamically and kinetically; (ii) ethylene and acetylene undergo [2+2] cycloaddition-like chemisorptions onto a rest atom-adatom pair; and (iii) all of these reactions adopt diradical mechanisms. This is in contrast to the [4+2] cycloaddition-like chemisorptions of conjugated dienes on a Si(100) surface and to the prototype [4+2] cycloadditions in organic chemistry, which were believed to adopt concerted reaction pathways. Of particular interest is the [4+2]-like cycloaddition of s-trans-1,3-butadiene, whose stereochemistry is retained during its chemisorption on the Si(111) surface.     

Competition and selectivity in the reaction of nitriles on ge(100)-2x1

We have experimentally investigated bonding of the nitrile functional group (R-Ctbd1;N:) on the Ge(100)-2x1 surface with multiple internal reflection infrared spectroscopy. Density functional theory calculations are used to help explain trends in the data. Several probe molecules, including acetonitrile, 2-propenenitrile, 3-butenenitrile, and 4-pentenenitrile, were studied to elucidate the factors controlling selectivity and competition on this surface. It is found that acetonitrile does not react on the Ge(100)-2x1 surface at room temperature, a result that can be understood with thermodynamic and kinetic arguments. A [4+2] cycloaddition product through the conjugated pi system and a [2+2] C=C cycloaddition product through the alkene are found to be the dominant surface adducts for the multifunctional molecule 2-propenenitrile. These two surface products are evidenced, respectively, by an extremely intense nu(C=C=N), or ketenimine stretch, at 1954 cm(-)(1) and the nu(Ctbd1;N) stretch near 2210 cm(-)(1). While the non-conjugated molecules 3-butenenitrile and 4-pentenenitrile are not expected to form a [4+2] cycloaddition product, both show vibrational modes near 1954 cm(-)(1). Additional investigation suggests that 3-butenenitrile can isomerize to 2-butenenitrile, a conjugated nitrile, before introduction into the vacuum chamber, explaining the presence of the vibrational modes near 1954 cm(-)(1). Pathways directly involving only the nitrile functional group are thermodynamically unfavorable at room temperature on Ge(100)-2x1, demonstrating that this functional group may prove useful as a vacuum-compatible protecting group.     

Adsorption Sequence of Multifunctional Groups: A Study on the Reaction Pathway and the Adsorption Structure of Homocysteine on the Ge(100) Surface

We investigated the adsorption mechanism of homocysteine (HS? CH₂? CH₂? CH(NH₂)? COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid′s functional groups using core‐level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” and the “SH‐dissociated OH‐dissociation‐bonded structure” were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (? SH), carboxyl group (? COOH), and amine group (? NH₂).     

Ylenes in the M(II)→Si(IV) (M=Si, Ge, Sn) coordination mode

The reaction of the methimazolyl (mt, i.e., 2-mercapto-1-methylimidazolide) substituted silane Si(mt)(4) with SnCl(2) and GeCl(2) in dioxane affords the paddlewheel-shaped complexes [ClSi(μ-mt)(4)MCl] (M=Sn (1) and Ge (2), respectively). These compounds represent the first crystallographically characterized hexacoordinate silicon complexes comprising a Sn or Ge atom in the Si coordination sphere. An attempt to synthesize the related silicon compound 3 [ClSi(μ-mt)(4)SiCl] instead afforded the trisilane [ClSi(μ-mt)(4)Si-SiCl(3)] (3a), which provides the first crystallographic evidence for the feasibility of oligosilanes with adjacent hexacoordinate Si atoms. One of the hexacoordinate Si atoms of 3a features the unprecedented (Si(2)S(4))Si skeleton. Natural bonding orbital (NBO) analyses of compounds 1, 2, 3a (and the target compound 3) revealed characteristics of M(II)→Si(IV) (for 2 and 3) or M(I)→Si(IV) (for 3a) dative bonding in the systems with M=Si and Ge, whereas compound 1 exhibits a covalent Sn(III)-Si(III) bond.     

The concerted and stepwise chemisorption mechanisms of isothiazole and thiazole on Si(100)?2?��?1 surface

The surface reaction pathways of isothiazole and thiazole on Si(100)?2?×?1 surface were theoretically investigated using multireference wavefunctions. In the case of isothiazole, the Si?CN dative adduct turned out to be the major surface product. In contrast, a direct reaction competition between a concerted [4?+?2]_CC cycloaddition and Si?CN dative adduct was found in the adsorption of thiazole. Therefore, it is concluded that the particular geometric arrangements of heteroatoms exhibit distinctly different initial surface reaction mechanisms.     

Density Functional Theory Study on Mechanism of Forming Spiro-Ge-heterocyclic Ring Compound from Me2Ge=Ge: and Acetaldehyde

The H₂Ge=Ge:, as well as and its derivatives (X₂Ge=Ge:, X=H, Me, F, Cl, Br, Ph, Ar, : : :) is a kind of new species. Its cycloaddition reactions is a new area for the study of germy-lene chemistry. The mechanism of the cycloaddition reaction between singlet Me₂Ge=Ge: and acetaldehyde was investigated with the B3LYP/6-31G* method in this work. From the potential energy profile, it could be predicted that the reaction has one dominant re-action pathway. The reaction rule is that the two reactants firstly form a four-membered Ge-heterocyclic ring germylene through the [2+2] cycloaddition reaction. Because of the 4p unoccupied orbital of Ge: atom in the four-membered Ge-heterocyclic ring germylene and the π orbital of acetaldehyde forming a π→p donor-acceptor bond, the four-membered Ge-heterocyclic ring germylene further combines with acetaldehyde to form an intermedi-ate. Because the Ge atom in intermediate happens sp3 hybridization after transition state, then, intermediate isomerizes to a spiro-Ge-heterocyclic ring compound via a transition state. The research result indicates the laws of cycloaddition reaction between Me₂Ge=Ge: and ac-etaldehyde, and lays the theory foundation of the cycloaddition reaction between H₂Ge=Ge: and its derivatives (X₂Ge=Ge:, X=H, Me, F, Cl, Br, Ph, Ar, : : :) and asymmetric π-bonded compounds, which are significant for the synthesis of small-ring and spiro-Ge-heterocyclic ring compounds.     

Ab initio study of the mechanism of forming a spiro‐heterocyclic ring compound involving Si and Ge from dichlorosilylene germylidene(Cl2SiGe:) and formaldehyde

The mechanism of the cycloaddition reaction between singlet dichlorosilylene germylidene (Cl₂Si?Ge:) and formaldehyde has been investigated with the CCSD(T)//MP2/6‐31G* method. From the potential energy profile, it could be predicted that the reaction has one dominant reaction pathway. The reaction rule presented is that the two reactants first form a four‐membered Si‐heterocyclic ring germylene through the [2 + 2] cycloaddition reaction. Because of the 4p unoccupied orbital of Ge atom in the four‐membered Si‐heterocyclic ring germylene and the π orbital of formaldehyde forming a π→p donor–acceptor bond, the four‐membered Si‐heterocyclic ring germylene further combines with formaldehyde to form an intermediate. Because the Ge atom in intermediate undergoes sp3 hybridization after transition state, then, the intermediate isomerizes to a spiro‐heterocyclic ring compound involving Si and Ge via a transition state. © 2012 Wiley Periodicals, Inc.     

Versatile stereoselective cycloadditions between heterocumulenes and phosphagermaallene Tip(tBu)Ge=C=PMes*: experimental and theoretical investigations

Phosphagermaallene Tip(tBu)Ge=C=PMes* 1 (Tip=2,4,6-triisopropylphenyl, Mes*=2,4,6-tri-tert-butylphenyl) reacts with phenyl isocyanate and tert-butyl isocyanate by a [2+2] cycloaddition that involves the Ge=C and C=O double bonds to afford 1-oxa-2-germacyclobutanes 2 and 3. With N,N'-dicyclohexylcarbodiimide, a [2+2] cycloaddition is observed between the Ge=C and C=N unsaturations to lead to 1-aza-2-germacyclobutane 6 with exocyclic P=C and C=N double bonds. In sharp contrast, 1 reacts with phenyl isothiocyanate, ethyl isothiocyanate, and carbon disulfide according to a [3+2] cycloaddition that involves the whole Ge=C=P unit and the C=S double bond to give transient phosphagermacarbenes (PGeHCs) 11, 12, and 13. These new PGeHCs undergo C-H insertions into one o-tBu group of Mes* (in the case of 11 and 12) or one o-iPr group of Tip (in the case of 13) with formation of tricyclic compounds 8, 9, and 10, respectively. The reaction mechanisms that involve 1 and the phenyl isocyanate and the phenyl isothiocyanate are described and their regioselectivity is explained by theoretical calculations.     

Ab initio study of the formation of bis-heterocyclic compound involving Si and Ge from dichlorosilylene germylidene (Cl2Si=Ge:) and ethene

The mechanism of the cycloaddition reaction between singlet state dichlorosilylene germylidene (Cl₂Si=Ge:) and ethene has been investigated with CCSD(T)//MP2/6-31G* method, from the potential energy profile, we predict that the reaction has one dominant reaction pathway. The presented rule of the reaction is that the two reactants firstly form a Si-heterocyclic four-membered ring germylene through the [2+2] cycloaddition reaction. Due to the sp ³ hybridization of the Ge: atom in Si-heterocyclic four-membered ring germylene, the Si-heterocyclic four-membered ring germylene further combined with the ethene to form a bis-heterocyclic compound with Si and Ge.     

The first example of a sigma(2)lambda(2)-dioxaphosphenium cation, stabilized by an intramolecular dative P(+) <-- S bond

[structure in text] The first example of a sigma(2)lambda(2)-dioxaphosphenium cation 5 bearing dioxathiophosphocin ring systems stabilized by an intramolecular dative P(+) <-- S bond and its reactivity with pyridine and cycloaddition reaction with 2,3-dimethylbutadiene are reported.     

Mechanically facilitated retro [4+2] cycloadditions

Poly(methyl acrylate)s (PMAs) of varying molecular weights were grown from a [4+2] cycloaddition adduct of maleimide with furan containing two polymerization initiators. Subjecting the corresponding PMA (>30 kDa) chains to ultrasound at 0 °C resulted in a retro [4+2] cycloaddition reaction, as observed by gel permeation chromatography (GPC) and UV-vis spectroscopy, as well as labeling of the liberated maleimide and furan moieties with appropriate chromophores featuring complementary functional groups. Similar results were obtained by sonicating analogous polymers that were grown from a thermally robust [4+2] cycloaddition adduct of maleimide with anthracene. The generation of anthracenyl species from these latter adducts allowed for the rate of the corresponding mechanically activated retro [4+2] cycloaddition reaction to be measured. No reduction in the number average molecular weight (M(n)) or liberation of the maleimide, furan, or anthracene moieties was observed (i) for polymers containing the cycloaddition adducts with M(n) < 20 kDa, (ii) for high molecular weight PMAs (M(n) > 60 kDa) featuring terminal cycloaddition adducts, or (iii) when the cycloaddition adducts were not covalently linked to a high molecular weight PMA. Collectively, these results support the notion that the aforementioned retro [4+2] cycloaddition processes were derived from a vectorially opposed mechanical force applied to adducts embedded within the polymer chains.     

Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Organocatalytic, enantioselective intramolecular [6+2] cycloaddition reaction for the formation of tricyclopentanoids and insight on its mechanism from a computational study

Diphenylprolinol silyl ether was found to be an effective organocatalyst for promoting the asymmetric, catalytic, intramolecular [6 + 2] cycloaddition reactions of fulvenes substituted at the exocyclic 6-position with a δ-formylalkyl group to afford synthetically useful linear triquinane derivatives in good yields and excellent enantioselectivities. The cis-fused triquinane derivatives were obtained exclusively; the trans-fused isomers were not detected among the reaction products. The intramolecular [6 + 2] cycloaddition occurs between the fulvene functionality (6π) and the enamine double bond (2π) generated from the formyl group in the substrates and the diphenylprolinol silyl ether. The absolute configuration of the reaction products was determined by vibrational circular dichroism. The reaction mechanism was investigated using molecular orbital calculations, B3LYP and MP2 geometry optimizations, and subsequent single-point energy evaluations on model reaction sequences. These calculations revealed the following: (i) The intermolecular [6 + 2] cycloaddition of a fulvene and an enamine double bond proceeds in a stepwise mechanism via a zwitterionic intermediate. (ii) On the other hand, the intramolecular [6 + 2] cycloaddition leading to the cis-fused triquinane skeleton proceeds in a concerted mechanism via a highly asynchronous transition state. (iii) The fulvene functionality and the enamine double bond adopt the gauche-syn conformation during the C-C bond formation processes in the [6 + 2] cycloaddition. (iv) The energy profiles calculated for the intramolecular reaction explain the observed exclusive formation of the cis-fused triquinane derivatives in the [6 + 2] cycloaddition reactions. The reasons for the enantioselectivity seen in these [6 + 2] cycloaddition reactions are also discussed.