Formation of surface-bound acyl groups by reaction of acyl halides on ge(100)-2x1

We have investigated the reaction of a series of acyl halides, including acetyl chloride, acetyl bromide, acetyl-d3 chloride, benzoyl chloride, and pivaloyl chloride, on Ge(100)-2x1 with multiple internal reflection infrared (MIR-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). Infrared spectra following saturation exposures of acetyl chloride and acetyl bromide to Ge(100)-2x1 at 310 K are nearly identical, both exhibiting strong nu(C=O) stretching peaks near 1685 cm-1 and no vibrational modes in the nu(Ge-H) region. These data provide strong evidence for the presence of a surface-bound acetyl group on Ge(100)-2x1, which results from a C-X dissociation reaction (where X=Cl, Br). For acetyl chloride, DFT calculations predict that the barrier to C-Cl dissociation is only 1 kcal/mol above a chlorine-bound precursor state and is considerably smaller than barriers leading to the [2+2] C=O cycloaddition and alpha-CH dissociation products. In addition to the C-X dissociation product, both infrared and photoelectron results point to the presence of a second structure for acetyl halides where the oxygen of the surface-bound acetyl group donates charge to a nearby surface atom. This interaction is not observed for benzoyl chloride and pivaloyl chloride.     

Ethylenediamine on Ge(100)-2 x 1: the role of interdimer interactions

We have investigated the reaction of the bifunctional molecule ethylenediamine on Ge(100)-2 x 1 using multiple internal reflection Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. Ethylenediamine exhibits different adsorption behavior than simple methylamines on the Ge(100)-2 x 1 surface. At low coverages, ethylenediamine undergoes dissociative chemisorption via an interdimer dual N-H dissociation reaction. As coverage increases, the N-H dissociation reaction is inhibited and formation of a Ge-N dative-bonded structure dominates.     

A [4+2]-like cycloaddition of methyl methacrylate on Si(100)-2 x 1

The attachment of methyl methacrylate (MMA) on Si(100)-2x1 was investigated using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and density functional theory (DFT) calculations. The HREELS spectra of chemisorbed MMA show the disappearance of characteristic vibrations of C=O (1725 cm(-1)) and C(sp(2))-H (3110, 1400, and 962 cm(-1)) coupled with the blue shift of the C=C stretching mode by 34 cm(-1) compared to those of physisorbed molecules. These results clearly demonstrate that both C=C and C=O in MMA directly participate in the interaction with the surface to form a SiCH(2)C(CH(3))=C(OCH(3))OSi species via a [4+2]-like cycloaddition. This binding configuration was further supported by XPS, UPS, and DFT studies.     

Structure and vibrational spectrum of the hydrogen-bonded system between 4-tert-butylphenol and N-bases: Ab initio and DFT studies

The structural and vibrational characteristics of the hydrogen-bonded system between 1,5,7-triazabicyclo [4.4.0] dec-5-ene (TBD) and 4-tert-butylphenol have been investigated employing ab initio and DFT calculations at different basis sets. The calculations show that the optimized structure of the studied system is cyclic. The corrected values of the dissociation energy for the hydrogen-bonded complex have been calculated in order to estimate its stability. The influence of the hydrogen bonding on the properties of the monomers (TBD and 4-tert-butylphenol) has been investigated. The hydrogen bonding between TBD and 4-tert-butylphenol leads to changes in the structural (bond lengths and angles) and vibrational (vibrational frequencies and infrared intensities) characteristics of the monomers. It was established that the TBD molecule is considerably deformed upon hydrogen bonding, while the deformation of the 4-t-BuPhOH is smaller. In agreement with the experiment, the calculations show that the stretching O-H vibration from 4-tert-butylphenol is shifted to lower frequency upon hydrogen bonding. The predicted frequency shift Deltanu(O-H) (-338cm(-1)) is in very good agreement with the experimentally observed (-351cm(-1)). In the same time the IR intensity of the nu(O-H) increases dramatically in the hydrogen-bonded system.     

Electronic structure of the hydroxo and methoxo oxometalate anions MO3(OH)- and MO3(OCH3)- (M = Cr, Mo, and W)

The electronic structure of the mononuclear hydroxo MO3(OH)- and methoxo MO3(OCH3)- Group 6 oxometalate anions (M = Cr, Mo, and W) were examined by photodetachment photoelectron spectroscopy and electronic structure calculations at the density functional and CCSD(T) levels of theory. All of the anions exhibited high electron binding energies (>4.9 eV), with the lowest-energy detachment features arising from oxygen 2p-based orbitals. The combined experimental and theoretical results allowed the change in molecular orbital energy levels to be investigated as a function of metal (Cr, Mo, or W) and ligand (-OH, -OCH3). A number of fundamental thermodynamic properties of the anions and corresponding neutrals were predicted on the basis of the theoretical calculations. The calculations indicate high O-H bond dissociation energies for MO2(OR)(O-H) (R = H, CH3) and MO3(O-H), consistent with their high Br?nsted acidities (just below that of H2SO4 in the gas phase) and the high ionization energies of their conjugate base anions. This suggests that the corresponding radicals should readily abstract H atoms from organic molecules.     

Mechanisms and energetics of hydride dissociation reactions on surfaces of plasma-deposited silicon thin films

We report results from a detailed analysis of the fundamental silicon hydride dissociation processes on silicon surfaces and discuss their implications for the surface chemical composition of plasma-deposited hydrogenated amorphous silicon (a-Si:H) thin films. The analysis is based on a synergistic combination of first-principles density functional theory (DFT) calculations of hydride dissociation on the hydrogen-terminated Si(001)-(2x1) surface and molecular-dynamics (MD) simulations of adsorbed SiH(3) radical precursor dissociation on surfaces of MD-grown a-Si:H films. Our DFT calculations reveal that, in the presence of fivefold coordinated surface Si atoms, surface trihydride species dissociate sequentially to form surface dihydrides and surface monohydrides via thermally activated pathways with reaction barriers of 0.40-0.55 eV. The presence of dangling bonds (DBs) results in lowering the activation barrier for hydride dissociation to 0.15-0.20 eV, but such DB-mediated reactions are infrequent. Our MD simulations on a-Si:H film growth surfaces indicate that surface hydride dissociation reactions are predominantly mediated by fivefold coordinated surface Si atoms, with resulting activation barriers of 0.35-0.50 eV. The results are consistent with experimental measurements of a-Si:H film surface composition using in situ attenuated total reflection Fourier transform infrared spectroscopy, which indicate that the a-Si:H surface is predominantly covered with the higher hydrides at low temperatures, while the surface monohydride, SiH((s)), becomes increasingly more dominant as the temperature is increased.     

Selective formation of cumulative double bonds (C[double bond]C[double bond]N) in the attachment of multifunctional molecules on Si(111)-7 x 7

The cumulative double bond (C[double bond]C[double bond]N), an important intermediate in synthetic organic chemistry, was successfully prepared via the selective attachment of acrylonitrile to Si(111)-7 x 7. The covalent binding of acrylonitrile on Si(111)-7 x 7 was studied using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM) and DFT calculations. The observation of the characteristic vibrational modes and electronic structures of the C[double bond]C[double bond]N group in the surface species demonstrates the [4 + 2]-like cycloaddition occurring between the terminal C and N atoms of acrylonitrile and the neighboring adatom-rest atom pair, consistent with the prediction of DFT calculations. STM studies further show the preferential binding of acrylonitrile on the center adatom sites of faulted halves of Si(111)-7 x 7 unit cells.     

Selective binding of the cyano group in acrylonitrile adsorption on Si(100)-2 x 1

The covalent binding of acrylonitrile (CH(2)=CH-C triple bond N) and the formation of a C=C-C=N structure on Si(100) have been investigated using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and density functional theory (DFT) calculations. For chemisorbed acrylonitrile, the absence of nu(C triple bond N) at 2245 cm(-1) and the appearance of nu(C=N) at 1669 cm(-1) demonstrate that the cyano group directly participates in the interaction with Si(100), which is further supported by XPS and UPS observations. Our experimental results and DFT calculations unambiguously demonstrate a [2 + 2] cycloaddition mechanism for acrylonitrile chemisorption on Si(100) through the binding of C triple bond N to Si dimers. The resulting chemisorbed monolayer with a C=C-C=N skeleton can serve as a precursor for further chemical syntheses of multilayer organic thin films in a vacuum and surface functionalization for in situ device fabrication.     

Proton transfer reactions on semiconductor surfaces

The concept of proton affinity on semiconductor surfaces has been explored through an investigation of the chemistry of amines on the Ge(100)-2 x 1, Si(100)-2 x 1, and C(100)-2 x 1 surfaces. Multiple internal reflection Fourier transform infrared (MIR-FTIR) spectroscopy, temperature programmed desorption (TPD), and density functional theory (DFT) calculations were used in the studies. We find that methylamine, dimethylamine, and trimethylamine undergo molecular chemisorption on the Ge(100)-2 x 1 surface through the formation of Ge-N dative bonds. In contrast, primary and secondary amines react on the Si(100)-2 x 1 surface via N-H dissociation. Since N-H dissociation of amines at semiconductor surfaces mimics a proton-transfer reaction, the difference in chemical reactivities of the Ge(100)-2 x 1 and Si(100)-2 x 1 surfaces toward N-H dissociation can be interpreted as a decrease of proton affinity down a group in the periodic table. The trend in proton affinities of the two surfaces is explained in terms of thermodynamics and kinetics. Solid-state effects on the C(100)-2 x 1 surface and the surface proton affinity concept are discussed based on our theoretical predictions.     

The photoinduced isomerization and its implication in the photo-dynamical processes in two simple Schiff bases isolated in solid argon

Two Schiff bases: 2-(1-(methylimino)methyl)-phenol (SMA) and its chlorosubstituted derivative 2-(1-(methylimino)methyl)-6-chlorophenol (SMAC), and SMA complexes with water were studied by infrared matrix isolation spectroscopy and DFT/B3LYP/6-311G++(2d,2p) quantum chemical calculations. SMA and SMAC bases trapped in an argon matrix from the vapor above the liquid and solid samples have the most stable enol conformation with intramolecular O-H···N bonding. Irradiation (λ > 320 nm) leads in both bases to a rotational isomerization reaction in which the scission of the O-H···N bond occurs and the C(H)NCH(3) and OH groups are turned by 180° around the C-C and C-O bonds, respectively. In SMAC a competitive photoreaction channel yields the trans-keto tautomer. The identification of the two SMAC photoproducts evidences that in the excited enol form of this compound two processes compete with each other: the rotational isomerization and intramolecular proton transfer (ESIPT). In the argon matrices doped with SMA and H(2)O the SMA-water complexes were identified and characterized spectroscopically. Interaction of SMA with one or two water molecules does not affect the photochemistry of SMA.     

Effect of dehydration on sulfate coordination and speciation at the Fe-(hydr)oxide-water interface: a molecular orbital/density functional theory and Fourier transform infrared spectroscopic investigation

The effect of dehydration on the coordination and speciation of sulfate at the Fe-(hydr)oxide-H2O interface was investigated using molecular orbital/density functional theory (MO/DFT) and Fourier transform infrared (FTIR) spectroscopy. IR frequency calculations were performed at the UB3LYP/6-31+G(d) level of theory for potential sulfate (bidentate bridging, monodentate, and H-bonded) and bisulfate (bidentate bridging and monodentate) surface complexes. MO/DFT calculated IR frequencies were compared to available IR literature results and attenuated total reflectance (ATR) FTIR spectra collected in our laboratory of sulfate adsorbed at the hematite-H2O interface. IR frequency calculations performed using the larger 6-311+G(d,p) basis set resulted in minor frequency shifts that did not dramatically alter the agreement with experiment. This investigation proposes that sulfate undergoes a speciation change as a function of surface dehydration. A generalized model for the speciation change is proposed as follows. (1) At the Fe-(hydr)oxide-H2O interface, sulfate adsorbs as a bidentate bridging or monodentate surface complex under most experimental conditions. (2) Upon surface dehydration, sulfate changes speciation to form bidentate bridging and/or monodentate bisulfate. However, surface dehydration does not yield 100% speciation change but leads to a mixture of sulfate and bisulfate. (3) The speciation change is reversible as a function of rehydration. The reversibility of the sulfate-bisulfate speciation change is chiefly determined by the local hydration environment of the O-H bond in bisulfate. Under dehydrated conditions, the O-H bond length is approximately 0.98 A. The bond length substantially increases (bond strength decreases) to approximately 1.03 A when the initial H-bond network is re-established through hydration, likely leading to deprotonation upon full mineral surface hydration.     

Matrix isolation infrared and ab initio study of the hydrogen bonding between formic acid and water

The infrared spectra of the formic acid-water complexes isolated in argon matrices are reported. Both supersonic jet expansion and a conventional effusive source followed by trapping in solid argon at 10K are used to obtain the matrices. The experimental IR spectra are compared to the data obtained from high level ab initio (MP2) and DFT (B3LYP) calculations with 6-311++G(d,p) and aug-cc-pVTZ basis sets. The complex formation results in red shifts in the C=O and O-H stretching vibrations and a blue shift in the C-O stretching vibration of formic acid. The O-H stretching modes of water also exhibit pronounced red shifts. Both the MP2 and B3LYP calculations located three minima corresponding to cyclic HCOOH...H2O complexes with two hydrogen bond interactions. The binding energies are -10.3, -5.1, and -3.5 kcal mol(-1), respectively, for the three complexes at the MP2/ aug-cc-pVTZ level, corrected for the basis set superposition error (BSSE) using the Boys-Bernardi counterpoise scheme. Comparison of the calculated frequencies of the three complexes with the matrix IR spectrum reveals that the lowest energy complex is formed. In addition, a complex of formic acid with two water molecules is observed.     

Infrared fingerprint spectroscopy and theoretical studies of potassium ion tagged amino acids and peptides in the gas phase

Infrared multiple-photon dissociation spectroscopy is effected on the K(+) tagged aromatic amino acids tyrosine and phenylalanine, as well as the K(+) tagged peptides bradykinin fragment 1-5 and [Leu]-enkephalin. The fingerprint (800-1800 cm(-1)) infrared spectra of these species are compared to density-functional theory (DFT) calculated spectra to determine whether the complex is in the charge solvation (CS) or salt bridge (SB) (i.e. zwitterionic) configuration. For the aromatic amino acids the CS structure is favored and the tridentate N/O/ring structure is found to be the preferred binding geometry for K(+). The experimental and theoretical evidence for bradykinin fragment 1-5 tagged with K(+) suggests that the SB structure is favored; the calculations indicate a head-to-tail looped structure stabilized by a salt bridge between the protonated guanidine group and the deprotonated C-terminus, which allows K(+) to sit in a binding pocket with five C=O electrostatic interactions. For K(+) tagged [Leu]-enkephalin the spectroscopic evidence is not as clear. While the calculations clearly favor a CS structure and the observation of a weak carboxylic acid C=O stretching band in the infrared spectrum matches this finding, the prominence of a band at 1600 cm(-1) renders the analysis more ambiguous, and hence the presence of some salt bridge ions cannot be excluded. Another striking feature in the [Leu]-enkephalin spectrum is the high infrared activity of the tyrosine side-chain modes, which can be clearly identified from comparison to the [Tyr + K](+) experimental spectrum, but which is not reproduced by the DFT calculations.     

Crown ether complexes with H₃O⁺ and NH₄⁺: proton localization and proton bridge formation

The complexes formed by crown ethers with hydronium and ammonium cations are of key relevance for the understanding of their supramolecular behavior in protic solvents. In this work, the complexes of the 15-crown-5 (15c5) and 18-crown-6 (18c6) ethers with H?O? and NH?? and their deuterated variants are investigated under isolated conditions. The study employs infrared multiple photon dissociation (IRMPD) vibrational spectroscopy and DFT B3LYP/6-31++G(d,p) calculations for conformational assignment. The 18c6 ether provides two energetically nearby C(3v) conformations with commensurate linear O-H···O and N-H···O bonds. The 15c5 ether ring adopts partially folded asymmetric pyramidal geometries, yielding one shorter linear H bond and two longer non-linear H bonds. Remarkably, an appreciable broadening of the IRMPD vibrational bands is observed for the 15c5-H?O?/D?O? complexes. This can be interpreted as a signature for partial sharing of the proton (or deuteron) between the water and the crown ether along the linear O-H···O intermolecular H bond, which is indeed particularly short for this complex.     

Infrared spectrum of 4-methoxypicolinic acid N-oxide: computation of asymmetric O-H stretching band

In this article we studied the strong intramolecularly hydrogen-bonded system 4-methoxypicolinic acid N-oxide. The potential energy surface V = V(rOH,rOO) and the corresponding dipole moment function were calculated using the DFT B3LYP/6-31+G(d,p) level of approximation. The time-independent vibrational Schr?dinger equation was solved using a rectangular grid basis set and shifted Gaussian basis set. The vibrational spectrum and metric parameters were also calculated. Effects of deuteration were considered. The calculated vibrational spectra were compared with the experimental spectra. The vibrational transition corresponding to asymmetric O-H stretching that occurs at about 1400 cm-1 compares well with the experimentally assigned O-H asymmetric stretching band centered at 1380 cm-1. The corresponding asymmetric O-D stretching band was predicted to be at 1154 cm-1, while the experimental O-D band was not assigned due to its very low intensity. Several overtones and hot transitions of significant intensities were located in the vicinity of the fundamental O-H stretching frequency, effectively broadening the infrared absorption attributed to the O-H stretching mode. This is in a good agreement with the observed broad protonic absorptions found in the infrared spectra of the title compound and its analogs. We have shown that the Gaussian basis set is the method of choice for a two-dimensional vibrational problem that requires several hundreds of vibrational basis functions and when high accuracy of the eigenvalues is required or when extending the calculations to more vibrational degrees of freedom. We have also demonstrated that for a large number of basis functions the Gramm-Schmidt orthogonalization procedure outperforms symmetric and canonical orthogonalization schemes.     

异丙醇的O-H伸缩振动泛频光谱和分子构像

使用高灵敏的光腔衰荡光谱(CavityRingDownSpectroscopy)技术测出了异丙醇的O-H伸缩v=4、5振动泛频光谱,每个振动能级都有三个吸收峰,被归属为分子构像的O-H伸缩泛频吸收.给出了光腔衰荡光谱的振动泛频吸收的谱带强度公式,并求得分子不同构像在不同振动能级的O-H伸缩泛频吸收的谱带强度;同时利用局域模理论,求得分子各O-H伸缩局域模振子的机械频率(X1)、非谐性(X2)以及解离能(D).用密度泛函(DFT)B3LYP/6-31+G*理论方法优化了分子的各种可能构像,验证了分子存在反式(trans)和偏转(gauche)两种稳定构像,计算的分子的O-H伸缩频率及构像稳定性同实验结果是一致的.     

Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces

Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C-O stretching mode of glucose and the observed O-H stretching mode of glucose that is shifted in position relative to the O-H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm(-1) upon the binding of glucose. Additionally, changes in the peak profile of the B-O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at approximately 1736 to 1742 cm(-1) depending on the identity of the bound sugar.     

Average orientation of a molecular rotor embedded in a Langmuir-Blodgett monolayer

A molecular rotor in which a naphthalene rotator is attached through a silicon atom to three fatty acid chains has been synthesized, and Langmuir-Blodgett techniques were used to deposit on silica surfaces monolayers of its calcium salt, both neat and diluted with stearic acid salts. The monolayer films have been characterized by ellipsometry and Fourier transform infrared (FT-IR) grazing-incidence attenuated total internal reflection (GATR) spectroscopy on Si-SiO(2) and by UV-vis absorption spectroscopy on SiO(2). The measurements were combined with calculations of the electronic (INDO/S) and vibrational (DFT) transition moment directions to deduce the average orientation of the rotor molecules, including the naphthalene ring, relative to the surface. In both neat and mixed films, the naphthalene ring is found to preferentially tilt toward the surface, enough that its rotation is most likely hindered. A comparable picture was obtained from molecular mechanics calculations on a mixed film of the naphthalene rotor and stearic acid.     

Probing the structural and electronic properties of small vanadium monoxide clusters

The structural evolution and bonding of a series of early transition-metal oxide clusters, V(n)O(q) (n = 3-9, q = 0,-1), have been investigated with the aid of previous photoelectron spectroscopy (PES) and theoretical calculations. For each vanadium monoxide cluster, many low-lying isomers are generated using the Saunders "Kick" global minimum stochastic search method. Theoretical electron detachment energies (both vertical and adiabatic) were compared with the experimental measurements to verify the ground states of the vanadium monoxide clusters obtained from the DFT calculations. The results demonstrate that the combination of photoelectron spectroscopy experiments and DFT calculation is not only powerful for obtaining the electronic and atomic structures of size-selected clusters, but also valuable in resolving structurally and energetically close isomers. The second difference energies and adsorption energies as a function of the cluster size exhibit a pronounced even-odd alternation phenomenon. The adsorption energies of one O atom on the anionic (6.64 → 8.16 eV) and neutral (6.41 → 8.13 eV) host vanadium clusters are shown to be surprisingly high, suggesting strong capabilities to activate O by structural defects in vanadium oxides.