Carbon-oxygen bond strength as a control of reaction kinetics: Phenol on Mo(110)

The reaction of phenol on Mo(110) has been studied using temperature programmed reaction and X-ray photoelectron spectroscopies. After desorption of multilayers and a weakly bound molecular species, decomposition produces the only reaction products observed: gaseous dihydrogen, surface carbon and surface oxygen. The O-H bond cleaves first at temperatures below 360 K to form surface phenoxide (C₆H₅O-), followed by C-H bond activation commencing at 370 K. C-O bonds are cleaved in the temperature range of 370 to 450 K. After annealing to 300 K, multiple species are detected on the surface by X-ray photoelectron spectroscopy. The cleavage of C-H bonds in the same temperature regime as C-O bonds is thought to lead to selective decomposition of phenol on Mo(110). The reaction of phenol is contrasted to that of a sulfur-containing analogue, benzenethiol, on the Mo(110) surface. The stability of the phenoxide intermediate with respect to carbon-heteroatom bond cleavage is greater than that of the corresponding phenyl thiolate formed from benzenethiol. Comparison of the reaction of phenol and benzenethiol demonstrates the importance of C-X (X = O,S) bond strength in determining the reactivity and selectivity of these molecules.     

Study on NDR property of nitro-Benzene SAMs by using UHV-STM

Recently, research on conducting molecules containing thiol functional groups, such as benzenethiol has been progressing. This conducting molecule is applicable to the study of NDR and switching properties of logic devices. The 4,4′-di(ethynylphenyl)-2′-nitro-1-(thioacetyl)benzene molecule contains a thiol functional group as in benzenethiol. Thus, we measured the property of NDR by using the self-assembly method in STM. Au substrate was exposed to a 1 mM solution of 1-dodecanethiol in ethanol for 24 h to form a monolayer. After thoroughly rinsing the sample, it was exposed to a 0.1 mM solution of 4,4′-di(ethynylphenyl)-2′-nitro-1-(thioacetyl)benzene in dimethylformamide (DMF) for 30 min and kept in the dark during immersion to avoid photo-oxidation. After assembly, we measured the electrical properties of self-assembly monolayers (SAMs) by using ultra-high-vacuum scanning tunneling microscopy (UHV-STM) and scanning tunneling spectroscopy (STS) [L.A. Bumm, J.J. Arnold, M.T. Cygan, T.D. Dunbar, T.P. Burgin, L. Jones ll, D.L. Allara, J.M. Tour, P.S. Weiss, Science 271 (1996) 1705]. As a result, we confirmed the property of NDR in a positive region between negative regions. The energy gap (E_g) obtained by using differential conductance (dI/dV–V) was verified through UV/visible. This molecule is applicable to the fabrication of molecular junctions.     

A computational study on the adsorption and ring cleavage of para-chlorophenol on anatase TiO2 surface

In this work, a computational technique based on semiempirical SCF MO method MSINDO, has been used for investigation of the adsorption and photocleavage of para-chlorophenol (p-CP) molecule on the anatase TiO₂ (0 0 1) and (1 0 0) surfaces. The surfaces have been modeled with two saturated clusters Ti₂₁O₅₈H₃₂ and Ti₃₆O₉₀H₃₆. The optimization of the perpendicular conformation of p-CP molecule relative to the anatase TiO₂ (1 0 0) surface, has resulted in a linkage of the molecule to the surface titanium atom via phenolic oxygen atom. We studied the aromatic ring cleavage by singlet oxygen (¹O₂) and superoxide radical anion () and accordingly, relevant mechanisms are suggested. The results reveal that the ring opening path of p-CP molecule on TiO₂ (1 0 0) surface, following the single electron transfer/ mechanism, is energetically more favourable than the ¹O₂/dioxetane mechanism.     

Photophysical studies of PET based acridinedione dyes with globular protein: Bovine serum albumin

Interaction of acridinedione dyes with model transport proteins, bovine serum albumin (BSA) in aqueous solution were investigated by fluorescence spectral studies. A fluorescence enhancement was observed on the addition of BSA to photoinduced electron transfer (PET) based acridinedione dyes, which posses C₆H₄(p-OCH₃) in the 9th position of the basic acridinedione ring. On the contrary, the addition of BSA to non-PET based acridinedione dyes with methyl or phenyl substitution in the 9th position does not result in any fluorescence enhancement. The enhancement in the fluorescence intensity is attributed to the suppression of PET process through space between -OCH₃ group and the acridinedione moiety is elucidated by steady state fluorescence measurements. The fluorescence anisotropy value (r) of 0.40 reveals that the motion of the dye molecule is highly constrained and is largely confined to the rigid microenvironment of the protein molecule. The binding constant (K) was found to be in the order of 6.0×10³ [M]⁻¹, which implies the existence of hydrophobic interaction between the PET based dye and BSA. Time resolved fluorescence lifetime measurements reveal that the PET based acridinedione dye preferably binds in the hydrophobic interior of BSA.     

Molecular conductance spectroscopy of conjugated,phenyl-based molecules on Au(111): the effect of end groups on molecular conduction

Four families of conjugated molecules, containing between one and three phenyl rings and having both thiol (–SH) and isocyanide (–NC) end groups, have been synthesized and assembled as monolayers on flat Au(111) substrates. The conductance spectra G(V) for these molecular wires were systematically measured in UHV conditions using scanning tunneling microscope techniques. The measured conductance spectra for the molecules having thiol end groups are compared to a recent theory for molecular conduction. The favorable comparison indicates that the important properties influencing the conductance of short, conjugated molecular wires having thiol end groups and forming self-assembled monolayers on a Au(111) surface have been successfully identified. The isocyanide molecules reveal a shift in Fermi level of the molecule as a function of phenyl ring number that is opposite to that observed for the thiol-terminated molecules. The trends in molecular conductance determined from this systematic study are summarized and discussed and provide insight into the role played by bonding end groups in electronic conduction.     

Photoinduced electron transfer in meso-nitrophenyl-substituted porphyrins and their chemical dimers

It is shown that steric interactions of volume substituents in the β-positions of pyrrole rings and the nitro group in mono-and di-meso-phenyl-substituted of octaethylporphyrins and their chemical dimers containing the electron-acceptor NO₂ group in the ortho-position of the phenyl ring at 295 K favor the direct overlap of molecular orbitals of the interacting subunits, resulting in the efficient quenching of fluorescence due to the direct electron transfer from the S₁ level to the lower-lying state via the “through-space” mechanism. The electron transfer in these compounds in nonpolar media (the rate constant k _et ^S =(3.2–9.5)×10⁹ s^?1 is nonadiabatic, whereas in strongly polar solvents (k _et ^S =2×10¹¹ s^?1) the adiabatic effects can be manifested. In compounds containing the NO₂ group in meta-or para-positions of the phenyl ring, the nonadiabatic electron transfer from the S ₁ level occurs less efficiently both in polar [k _et ^S =(0.2–5)×10¹⁰ s^?1] and nonpolar media [k _et ^S =(0.1–1.0)×10⁷ s^?1]. In this case, the electron transfer involves molecular orbitals of phenyl (the “through-bond” mechanism), and its efficiency depends on the orbital electron density in the meta-and para-positions of the phenyl ring. Based on the experimental data obtained and analysis of the electron transfer within the framework of the Marcus theory, the energy scheme of relaxation processes of the electronic energy in the compounds under study involving charge transfer states is suggested.     

Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin‐A2

Combretastatin‐A2 (CA2), a potential anticancer drug in advanced preclinical development, is extracted from the medicinal plant C ombretum caffrum. The NIR‐FT Raman and FT‐IR spectral studies of the molecule were carried out and a b initio calculations performed at the B3LYP/6‐31G(d) level to derive the equilibrium geometry as well as the vibrational wavenumbers and intensities of the spectral bands. The vibrational analysis showed that the molecule has a similar geometry as that of c is‐stilbene, and has undergone steric repulsion resulting in twisting of the phenyl ring with respect to the ethylenic plane. Vibrational analysis was used to investigate the lowering of the stretching modes, and enhancement of infrared band intensities of the C–H stretching modes of Me2 may be attributed to the electronic effects caused by back‐donation and induction from the oxygen atom. Analysis of phenyl ring modes shows that the CA2 stretching mode 8 and the aromatic C–H in‐plane bending mode are equally active as strong bands in both IR and Raman spectra, which can be interpreted as the evidence of intramolecular charge transfer (ICT) between the OH and OCH₃groups via conjugated ring path and is responsible for bioactivity of the molecule. Copyright © 2008 John Wiley & Sons, Ltd.     

Novel contrast mechanisms in photoelectron microscopy

Two previously undiscussed contrast mechanisms in Auger and photoelectron microscopy, namely photoelectron diffraction contrast and molecular orbital orientation contrast, are presented. The former contrast mechanism is based on the phenomenon of photoelectron diffraction and forward focusing of Auger and photoelectrons, the latter is based on near-edge absorption fine structure (NEXAFS) spectroscopy and stems from the dependence of the NEXAFS resonance intensity on the orientation of the electric field vector of the incoming linearly polarized light with respect to the molecular orbital associated with this resonance. The applicability of both contrast mechanisms was demonstrated using a nickel polycrystal and a monolayer of benzoic acid (BA) on this polycrystal as test systems. Within the photoelectron diffraction approach well-resolved images of the individual microcrystallites on the surface of Ni polycrystal were obtained by using the photoelectrons from both the localized core level (Ni 2p_3/2) and the free-electron-like valence band. Within the molecular orbital orientation approach the well-resolved images of the azimuthally aligned BA molecules on the surface of the (110) microcrystallites incorporated into a Ni polycrystal were acquired. In these experiments the photon energy was tuned to the excitation energy of the π* orbital of the phenyl ring, which is a constituent of a BA molecule, and the C1s → π* excitation was monitored by the carbon KLL Auger electrons. The distinction between photoelectron diffraction and molecular orbital orientation contrast mechanisms within an imaging experiment is discussed.     

Structurally Simple Ferrocene Derivatives for Selective Cadmium Sensing

Three new ferrocene based Schiff bases 4-{[(E)-ferrocenylmethylidene] amino}benzenethiol (1b), 3-{[(E)-ferrocenylmethylidene]amino} benzenethiol (1c), 2-{[(E)-ferrocenylmethylidene]amino} benzenethiol (1d) have been synthesized to study their sensor property to various metal ions. It has been observed that 1b is highly fluorescent and its fluorescence changes in presence of metal ions. It was further observed that compound 1b is highly selective towards Cd²⁺ ion in solution.     

pH‐dependent surface‐enhanced Raman scattering observation of sulfanilamide on the silver surface

Monolayers of sulfanilamide on metallic surface can serve as an ideal model for understanding the interaction mechanism between the metal and the sulfanilamide molecule. In the present paper, the surface‐enhanced Raman scattering (SERS) technique was employed to obtain the SERS spectra of sulfanilamide monolayers formed on the silver surface under different pH values. Assignments of the spectra were carried out with the aid of density functional theory (DFT) calculations (BLYP/6‐311G). It can be found that the adsorption function of sulfanilamide on the silver surface was influenced by the pH value. The fully protonated sulfanilamide molecule adsorbed on the silver surface through N¹³H₂ group and the benzene ring anchored in a relatively perpendicular manner leading to N⁷H₂ and S¹⁰O₂ groups near the surface, while the completely deprotonated sulfanilamide molecule attached on the silver surface via N⁷H₂ and the benzene ring was perpendicular to, and the N¹³H₂ and S¹⁰O₂ groups were far from the silver surface. Copyright © 2009 John Wiley & Sons, Ltd.     

Surface state control of III–V semiconductors using molecular modification

An attempt to control surface electronics of III–V semiconductor using wet chemical processes has been performed. Here, we report results on the use of self-assembled monolayers (SAMs) of organic molecules on (0 0 1) GaAs surface. Octadecanethiol (ODT) and benzenethiol (BT) have been the choice in the present study.GaAs wafers were modified by thiol molecules on the flat surface after the native oxide layers are removed by chemical etching under optimized conditions. The change in the electronic properties was measured in terms of transport properties via the SAM layer by conductive probe atomic force microscopy. The current–voltage characteristics thus obtained show that ODT functions as a tunnel barrier while BT is conductive due to the presence of π-electrons. As a result, we can control the electronic states of GaAs–molecule interface for realizing novel device structures by the selection of functional molecules.     

Physisorption of metal carbonyls on Cu(100)

Chromium hexacarbonyl (Cr(CO)₆) and cyclopentadienyl rhodium dicarbonyl ((η⁵ − C₅H₅)Rh(CO)₂) were physisorbed on the Cu(100) surface and their molecular orientations were deduced from their reflection-absorption infrared (RAIR) spectra. No thermal decomposition of the compounds was observed. Physisorbed Cr(CO)₆ exhibited a substantial degree of dipole-dipole coupling within the adlayer, which was successfully disrupted by coadsorption in Ar at 23 K. The large absorption coefficient of the T_1u mode and the different boundary conditions of this ultrathin layer on a surface resulted in the observation of the longitudinal optical mode, confirming that the molecule is oriented with one carbonyl group adjacent to the surface. A Lyndane-Sachs-Teller splitting of 75 cm⁻¹ was observed for the T^1u mode. The physisorbed layer of (η⁵ − C₅H₅)Rh(CO)₂ did not exhibit strong dipole-dipole coupling, and was oriented with the C₅H₅ (Cp) ring parallel to the surface.     

Phenyl substituted Mg porphyrazines: The effect of annulation of a chalcogen-containing heterocycle on the spectral-luminescent properties

We have performed complex experimental and theoretical investigations of the spectral-luminescent properties and electronic structure of new phthalocyanine analogs, Mg octaphenylporphyrazine and its derivatives with an annulated thiadiazole or selenadiazole ring instead of two phenyl groups. Fluorescence characteristics have been determined at 293 and 77 K: emission, excitation, and fluorescence polarization spectra; fluorescence quantum yield ?? _F , and lifetime ?? _F . Annulation of a five-membered chalcogen-containing heterocycle leads to splitting of the long-wavelength absorption band Q(0-0) and to the bathochromic shift of its longest wavelength component Q _x (0-0), which increase upon passage from S to Se. At the same time, the fluorescence quantum yield ?? _F and lifetime ?? _F decrease, which is related to the intramolecular heavy-atom effect. The geometric structure of the ground state of the Mg porphyrazine molecules has been determined based on the density functional theory (DFT), and excited electronic states have been calculated with modified parametrization of the INDO/S method, INDO/Sm. Semiquantitatively, the calculated level positions of the lowest Q states and spectral shifts of Mg octaphenylporphyrazine and S-derivative agree with experimental data. For the range of the Soret band, calculated transition energies and their intensity distributions substantially depend on the dihedral angle ?? between a phenyl ring and porphyrazine macrocycle. We show that, based on calculations at the angle ?? = 60°, bands in the observed absorption spectra can be assigned with an accuracy of ??2000 cm^?1.     

RAIRS investigations on the orientation and intermolecular interactions of adenine on Cu(1 1 0)

The adsorption of the DNA base adenine (C₅N₅H₅) on Cu(1 1 0) has been investigated as a function of coverage and temperature using reflection absorption infrared spectroscopy. These data provide important information on the nature of the local adsorbed complex and the intermolecular lateral interactions that come into play at high coverages. The RAIR spectra are consistent with an adsorption geometry in which the molecular ring is substantially tilted from the surface plane and in which the two amino hydrogens are equidistant from the surface, thus rationalising the appearance of a very strong βNH₂ scissoring mode, along with the activity of in-plane vibrational modes and the observation of the symmetric ν_symNH₂ stretch, but not the asymmetric ν_asymNH₂ stretch. In addition, coordination to the metal surface is proposed to occur at the N(9) position with a possible additional interaction through the N(3) position, both of which are the favoured coordination points in the metal complexes of adenine. This is a strong interaction and leads to a highly stable adsorbed layer. Our data also provide the first direct evidence of hydrogen bonding in the adlayer as coverage is increased, attributed to interactions between the amino group of one molecule and the N(1) and N(7) positions of a neighbouring species. When adsorption is carried out at room temperature, a very heterogeneous adlayer is created in which a diversity of molecular aggregates co-exist. However, upon annealing, a more ordered hydrogen bonded adlayer is formed in which one type of hydrogen bonding assembly is preferred. Finally, we propose that the hydrogen bonded assemblies created at a surface probably involve bent hydrogen bonds which arise from a compromise between the strong molecule-metal interactions that orientate the molecule and weaker lateral hydrogen bonding interactions that dictate the two-dimensional architecture.     

The adsorption of toluene on V-Sb oxides. Theoretical aspects

Toluene adsorption reactions on the (1 1 0) surface of VSbO₄ have been analyzed following the changes in the electronic structure of the hydrocarbon molecule and metal cation sites of the oxide using the Just Another Extended Hückel Molecular Orbital Program (JAEHMOP) code. The bonding character of these interactions has also been studied in the same theoretical framework. The calculations indicate that the exothermic hydrocarbon parallel interaction on Sb-V sites results in the weakening of one of the C-H bonds of the methyl fragment. This leads to a H-abstraction that involves the participation of a Sb-cation. Both methyl and phenyl fragments decrease their electronic population and so does the V-cation site. Most of these electrons are transferred to other V atoms in the bulk solid. As a result the LUMO of the toluene-oxide system fully populates. The analysis reveals that methyl-Sb bonding interactions mainly involve C_2px and H_1s orbitals with Sb_5s orbital, while non-bonding phenyl-V interactions involve C_2px orbitals with V_3dx²−y² orbital. This last interaction facilitates the desorption of the benzyl species after H-abstraction.     

Theoretical study of optical and electronic properties of p-terphenyls containing cyano substituents as promising light-emitting materials

Recently, p-terphenyls containing alkoxylated backbones with or without CN groups on either the central phenyl ring or peripheral rings were synthesized and their photo-luminescent properties were studied. Herein, semi-empirical AM1 and density functional theory (DFT) B3LYP calculations with the 6-31G* basis set have been performed to optimize structure for the ground state and the semi-empirical ZINDO calculations have been used to determine the maximum absorption (λ_abs^max) and emission wavelengths (λ_emi) for 19 p-terphenyls. The steric effect is assigned to be responsible for the calculated λ_abs^max and λ_emi shifts and the CN group at the central phenyl with ortho-substitution and at peripheral phenyl rings with para-substitution can also significantly influence these spectra. According to experimental results, the p-terphenyls with CN groups may have a lower energy of LUMO, and thus, we investigated the influence of the substitution position and the number of CN groups on the p-terphenyl moiety. The calculated optical and electronic properties provide important information on the behavior of the corresponding Organic light-emitting diode device (OLED). The suggested theoretical calculation protocol can be employed to predict electro-luminescent characteristics of other materials, and further, to design novel materials for OLED.     

Adsorption of water molecule on (001) and (110) surfaces of MgH2

First principle calculations have been performed to explore the adsorption characteristics of water molecule on (001) and (110) surfaces of magnesium hydride. The stable adsorption configurations of water molecule on the surfaces of MgH₂ were identified by comparing the total energies of different adsorption states. The (110) surface shows a higher reactivity with H₂O molecule owing to the larger adsorption energy than the (001) surface, and the adsorption mechanisms of water molecule on the two surfaces were clarified from electronic structures. For both (001) and (110) surface adsorptions, the O p orbitals overlapped with the Mg s and p orbitals leading to interactions between O and Mg atoms and weakening the O–H bonds in water molecule. Due to the difference of the bonding strength between O and Mg atoms in the (001) and (110) surfaces, the adsorption energies and configurations of water molecule on the two surfaces are significantly different.     

The influence of electronic and structural factors on the photoinduced electron transfer in sterically strained <Emphasis Type="Italic">meso</Emphasis>-nitrophenyl-substituted porphyrins

The electronic and structural factors affecting the efficiency of the photoinduced electron transfer in meso-nitrophenyl-substituted octaethylporphyrins are theoretically analyzed by semiempirical methods of quantum chemistry. It is shown that the experimental differences between the rate constants of electron transfer associated with the change in the position of the nitro group in the meso-phenyl ring (ortho, meta, or para positions) are determined by such factors as torsional vibrations of the phenyl ring around the single C₁-C_m bond, electronic properties of the phenyl group, rotations of the nitro group around the single C-N bond, and out-ofplane deformations of the porphyrin macrocycle. It is ascertained that the matrix elements of electronic interactions and the energies of excited charge-transfer states depend substantially both on the position of the nitro group in the meso-phenyl ring and on intramolecular vibrations of the phenyl and the nitro groups. In nonpolar media, the fluorescence quenching in the compounds under study occurs mainly due to the admixture of chargetransfer excitations to the lowest S ₁ state of porphyrin. Upon increasing polarity, the main channel of deactivation of excited singlet states is direct photoinduced electron transfer either through space (the ortho position) or through a bond involving the participation of orbitals of the phenyl spacer (the meta and para positions).     

Electrochemical scanning tunneling microscopy examination of the structures of benzenethiol molecules adsorbed on Au(1 0 0) and Pt(1 0 0) electrodes

In situ electrochemical scanning tunneling microscopy (STM) has been used to examine the structures of benzenethiol adlayers on Au(1 0 0) and Pt(1 0 0) electrodes in 0.1 M HClO₄, revealing the formation of well-ordered adlattices of Au(1 0 0)-(√2 × √5) between 0.2 and 0.9 V and Pt(1 0 0)-(√2 × √2)R45° between 0 and 0.5 V (versus reversible hydrogen electrode), respectively. The coverage of Au(1 0 0)-(√2 × √5) is 0.33, which is identical to those observed for upright alkanethiol admolecules on Au(1 1 1). In comparison, the coverage of Pt(1 0 0)-(√2 × √2)R45° - benzenethiol is 0.5, much higher than those of thiol molecules on gold surfaces. This result suggests that benzenethiol admolecules on Pt(1 0 0) could stand even more upright than those on Au(1 0 0). All benzenethiol admolecules were imaged by the STM as protrusions with equal corrugation heights, suggesting identical molecular registries on Au(1 0 0) and Pt(1 0 0) electrodes, respectively. Modulation of the potential of a benzenethiol-coated Au(1 0 0) electrode resulted in irreversible desorption of admolecules at E ? 0.1 V (vs. reversible hydrogen electrode) and oxidation of admolecules at E ? 0.9 V. In contrast, benzenethiol admolecule was not desorbed from Pt(1 0 0) at potentials as negative as the onset of hydrogen evolution. Raising the potential rendered deposition of more benzenethiol molecules before oxidation of admolecules commenced at E > 0.9 V.     

Resonance Raman spectrum of selenium thin film

The resonance Raman spectrum of a selenium thin film at 20 K has been measured with the 514.5 nm excitation. A series of overtones, nv₇ (n = 1–5), v₂ + nv₇ (n = 0–3) and v₁₀ have been observed where v₇, v₂ and v₁₀ are the fundamental vibrations of the Se₈ ring molecule. The broadness of these bands at 20K suggests that the thin film contains randomly orientated Se₈ ring molecules.