Rapid vapor-phase fabrication of organic-inorganic hybrid superlattices with monolayer precision

We report a new layer-by-layer growth method of self-assembled organic multilayer thin films based on gas-phase reactions. In the present molecular layer deposition (MLD) process, alkylsiloxane self-assembled multilayers (SAMs) were grown under vacuum by repeated sequential adsorptions of C=C-terminated alkylsilane and titanium hydroxide. The MLD method is a self- limiting layer-by-layer growth process, and is perfectly compatible with the atomic layer deposition (ALD) method. The SAMs films prepared exhibited good thermal and mechanical stability, and various unique electrical properties. The MLD method, combined with ALD, was applied to the preparation of organic-inorganic hybrid nanolaminate films in the ALD chamber. The organic-inorganic hybrid superlattices were then used as active mediums for two-terminal electrical bistable devices. The advantages of the MLD method with ALD include accurate control of film thickness, large-scale uniformity, highly conformal layering, sharp interfaces, and a vast library of possible materials. The MLD method with ALD is an ideal fabrication technique for various organic-inorganic hybrid superlattices.     

Well-ordered self-assembled monolayers created via vapor-phase reactions on a monolayer template

The reaction of vapor-phase alkyl isocyanates (O=C=N-(CH2)n-1CH3) with OH-terminated alkanethiol template monolayers on Au produces well-organized self-assembled monolayers, containing intrachain carbamate linkages (Au/S(CH2)16O(C=O)NH(CH2)n-1CH3, where n = 1-8, 11, and 12). X-ray photoelectron spectroscopy, contact angle goniometry, and reflection absorption infrared spectroscopy suggest that the template surface completely reacts with the isocyanates yielding a monolayer that contains an interchain hydrogen-bonded carbamate network. Spectroscopic data indicates that the alkyl underlayer remains well ordered following reaction with the isocyanates. The order of the overlayer and the hydrogen-bonding interactions between adjacent chains increase as a function of the alkyl isocyanate chain length, n. The overlayer appears to be well ordered for n > or = 5.     

Delocalized electron resonance at the alkanethiolate self-assembled monolayer/Au(111) interface

We probe the electronic structure of alkanethiolate self-assembled monolayers (SAMs) on Au(111) using two-photon photoemission spectroscopy. We observe a dispersive unoccupied resonance close to the vacuum level with a lifetime shorter than 30 fs. The short lifetime and the insensitivity of the energy level and dispersion to molecular length (and thus layer thickness) suggest that the probability density of the electron wave function is concentrated inside the molecular layer close to the SAM/Au interface. Such an interfacial resonance results from the image like potential at the SAM/Au interface.     

由烷基硫醇组成的三元混合膜结构与性质研究

本文采用共吸附法制备了由戊硫醇(PT),癸硫醇(DT)和十六烷基硫醇(HDT)组成的三元混合膜,通过循环伏安,X-射线光电子能谱,扫描隧道显微镜(STM)和导电原子力对其结构及性质进行了表征。研究表明硫醇分子通过Au-S键在金电极上形成了一层致密的单分子膜,组装膜表面组成与其在组装液中的摩尔浓度有关。混合膜中各组分形成独立的相区,具有不同的电子传递能力。该研究为未来纳米器件的开发提供更多样化的表面以及更加详实的理论依据。     

Theoretical study of the effect of surface density on the dynamics of Ar + alkanethiolate self-assembled monolayer collisions

We present a classical-trajectory study of energy transfer in collisions of Ar atoms with alkanethiolate self-assembled monolayers (SAMs) of different densities. The density of the SAMs is varied by changing the distance between the alkanethiolate chains in the organic monolayers. Our calculations indicate that SAMs with smaller packing densities absorb more energy from the impinging Ar atoms, in agreement with recent molecular-beam scattering experiments. We find that energy transfer is enhanced by a decrease in the SAM density because (1) less dense SAMs increase the probability of multiple encounters between Ar and the SAM, (2) the vibrational frequencies of large-amplitude motions of the SAM chains decrease for less dense SAMs, which makes energy transfer more efficient in single-encounter collisions, and (3) increases in the distance between chains promote surface penetration of the Ar atom. Analysis of angular distributions reveals that the polar-angle distributions do not have a cosine shape in trapping-desorption processes involving penetration of the Ar atom into the alkanethiolate self-assembled monolayers. Instead, there is a preference for Ar atoms that penetrate the surface to desorb along the chain-tilt direction.     

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover

We propose a conformational search method to find a global minimum energy structure for protein systems. The simulated annealing is a powerful method for local conformational search. On the other hand, the genetic crossover can search the global conformational space. Our method incorporates these attractive features of the simulated annealing and genetic crossover. In the previous works, we have been using the Monte Carlo algorithm for simulated annealing. In the present work, we use the molecular dynamics algorithm instead. To examine the effectiveness of our method, we compared our results with those of the normal simulated annealing molecular dynamics simulations by using an α-helical miniprotein. We used genetic two-point crossover here. The conformations, which have lower energy than those obtained from the conventional simulated annealing, were obtained.     

Synthesis of nanoparticles using vapor-phase decomposition of copper(II) acetylacetonate

Experimental data on the synthesis of crystalline Cu, Cu₂O, and CuO nanoparticles obtained earlier by the vapor-phase decomposition of copper(II) acetylacetonate (Cu(acac)₂) were systematized and generalized. Studies were performed using a laminar flow reactor at atmospheric pressure within the ranges of precursor partial vapor pressure P _prec = 0.06–44 Pa and reactor temperature from 432 to 1216°C. The decomposition of Cu(acac)₂ was studied in an inert nitrogen atmosphere and in the presence of various reagents (water vapors, H₂, O₂, and CO). The composition of synthesized particles varied from pure copper to its oxides (Cu₂O and CuO) depending on experimental conditions and used reagents. A semi-empirical kinetic model was proposed for describing the product dynamics. The hypothesis on the predominant role of copper dimers in a particles growth was stated. It was established that the composition of products is determined by the surface reactions on growing particles and is dependent on the ratio between the concentrations of the gaseous reagents. Calculated phase diagrams of the products of Cu(acac)₂ decomposition in the presence of various reagents were in good agreement with experimental data. The proposed method of construction of the phase diagram of decomposition products can be employed for other systems. It was established that, upon the Cu(acac)₂ decomposition in the presence of CO, carbon nano-onions were formed in addition to copper nanoparticles.Translated from Kolloidnyi Zhurnal, Vol. 67, No. 1, 2005, pp. 5–25.Original Russian Text Copyright © 2005 by Nasibulin, Shurygina, Kauppinen.     

Synthesis and structures of aluminum alkanethiolate complexes

The homoleptic aluminum thiolate complex [Al(mu-S-t-Bu)(S-t-Bu)(2)](2) was prepared by reacting AlBr(3) with NaS-t-Bu while the analogous 2-propanethiolate complex [Al(mu-S-i-Pr)(S-i-Pr)(2)](2) was synthesized by reacting AlH(3)(OEt(2)) with i-PrSH. In the solid state, the dimers have tetrahedral Al atoms and anti-Al(mu-SR)(2)Al four-member rings. The attempted synthesis of [Al(mu-S-t-Bu)(S-t-Bu)(2)](2) by reacting Al(N-i-Pr(2))(3) with t-BuSH in THF solvent yielded the thermally stable THF adduct Al(S-t-Bu)(3)(THF). The same reaction in diethyl ether solvent produced a mixture of [Al(mu-mgr;-S-t-Bu)(S-t-Bu)(2)](2) and the salt [i-Pr(2)NH(2)][Al(S-t-Bu)(4)]. In the solid-state structure of the salt, the anion [Al(S-t-Bu)(4)](-) has a distorted tetrahedral geometry. Reactions of [Al(NMe(2))(3)](2) and AlH(3)(NMe(2)Et) with the alkanethiols yielded stable amine adducts Al(SR)(3)(R'NMe(2)) (R = i-Pr or t-Bu; R' = H or Et). The ligand adducts Al(S-i-Pr)(3)(HNMe(2)) and Al(S-t-Bu)(3)(THF) have distorted trigonal pyramidal geometries in the solid state. Three of the new compounds, [Al(mu-S-i-Pr)(S-i-Pr)(2)](2) and Al(SR)(3)(HNMe(2)) (R = i-Pr or t-Bu), are viable precursor candidates for the chemical vapor deposition of aluminum sulfide films because they are thermally stable, volatile liquids at moderate temperatures.     

Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model

This paper proposed an improved simulated annealing (ISA) algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. In the algorithm, we provided a general formula used for producing initial solution, and designed a multivariable disturbance term, relating to the parameters of simulated annealing and a tuned constant, to generate neighborhood solution. To avoid missing optimal solution, storage operation was performed in searching process. We applied the algorithm to test artificial protein sequences from literature and constructed a benchmark dataset consisting of 10 real protein sequences from the Protein Data Bank (PDB). Otherwise, we generated C_α space-filling model to represent protein folding conformation. The results indicate our algorithm outperforms the five methods before in searching lower energies of artificial protein sequences. In the testing on real proteins, our method can achieve the energy conformations with C_α-RMSD less than 3.0 Å from the PDB structures. Moreover, C_α space-filling model may simulate dynamic change of protein folding conformation at atomic level.     

Chemical pathways in the interactions of reactive metal atoms with organic surfaces: vapor deposition of Ca and Ti on a methoxy-terminated alkanethiolate monolayer on Au

In situ time-of-flight secondary ion mass spectrometry, infrared spectroscopy, and X-ray photoelectron spectroscopy measurements have been used to characterize the interfacial chemistry that occurs upon physical vapor deposition of Ti and Ca atoms onto a -OCH(3) terminated alkanethiolate self-assembled monolayer (SAM) on Au{111}. While the final result for both metals is near-exhaustive degradation of the methoxy terminal group and partial degradation of the alkyl chains to inorganic products such as carbides, hydrides, and oxides, the reaction mechanisms differ significantly. Titanium reacts in parallel with the -OCH(3) and -CH(2)- units, extensively degrading the latter until a metallic overlayer forms preventing further degradation. At this point, there is a cessation of the Ti-SAM reactions. In contrast, Ca is initially consumed by the -OCH(3) terminal group via a reaction mechanism involving two -OCH(3) groups; subsequent depositions lead to alkyl chain degradation, but at a rate slower than that for Ti deposition. These results demonstrate the subtle differences in chemistry that can arise in the vapor deposition of reactive metals, and have important implications for the behavior of electrical interfaces in organic and molecular devices made with Ti or Ca top contacts.     

Hybridization of oligonucleotide by using DNA self-assembled monolayer

The interaction between DNA immobilized on surface and oligonucleotides at the interface is important in detection and diagnostic processes. However, it is difficult to immobilize DNA with maintaining its activity and to realize an efficient hybridization in previous methods. Here, to establish a novel DNA-functionalized surface, the DNA self-assembled monolayer (SAM) was constructed on a gold substrate using thiolated DNA composed of double-stranded (ds) and single-stranded (ss) portion. The DNA SAM was characterized by surface plasmon resonance (SPR), XPS. The hybridization of ss portion of DNA was attempted using the SAM, and in situ monitored by SPR. XPS measurement indicated that the thiolated DNA could form a stable monolayer on a gold substrate through sulfur–gold interaction. SPR measurement implied that the long axis of the DNA standing on the substrate. These results indicated formation of the DNA SAM on the substrate. Hybridization of target DNA containing a complementary sequence for the probe portion was observed by SPR. Moreover, one mismatch of oligonucleotide could be distinguished using the DNA SAM. The SPR result indicates that hybridization of target DNA and probe DNA on the DNA SAM occurs on the DNA SAM.     

Effects of shearing flow with inertia on monolayer mesoscale structure

In an experimental flow system capable of imparting a well-controlled shear-rate distribution with inertia to a monolayer consisting of coexisting phases, we have studied the resulting phase morphology and domain fragmentation. These evolve on distinct time scales: the viscous time associated with the viscosity in the bulk and the Marangoni stress and the fragmentation/relaxation time associated with the phase morphology. A relationship between the microstructure (line tension) and macroflow (shear rate) determining the meso length scale of the coexisting phase domains has been deduced from dimensional analysis and was found to correlate well with the quantitative experimental observations.     

Mechano-chemical stability of gold nanoparticles coated with alkanethiolate SAMs

Molecular dynamics simulations are used to probe the structure and stability of alkanethiolate self-assembled monolayers (SAMs) on gold nanoparticles. We observed that the surface of gold nanoparticles becomes highly corrugated by the adsorption of the SAMs. Furthermore, as the temperature is increased, the SAMs dissolve into the gold nanoparticle, creating a liquid mixture at temperatures much lower than the melting temperature of the gold nanoparticle. By analyzing the mechanical and chemical properties of gold nanoparticles at temperatures below the melting point of gold, with different SAM chain lengths and surface coverage properties, we determined that the system is metastable. The model and computational results that provide support for this hypothesis are presented.     

Two-dimensional crystal structure of a quaterthiophene-alkanethiol self-assembled monolayer on gold

We investigated the fine structure of a self-assembled monolayer of dodecanethiol functionalized by alpha-quaterthiophene on gold (alpha-4TC 12H 24SH). The molecular orientation, quantified using polarization modulation infrared reflection-absorption spectroscopy, was studied as a function of the adsorption time. The alpha-4T moieties arrange in the upright position on the surface as the adsorption time increases, while the alkyl chain organization remains poor. Here we quantify the orientation of the self-assembled monolayer and, more significantly, reveal through surface X-ray diffraction that after a long incubation period (12 h) the alpha-4T on the gold surface adopts a 2D crystal structure.     

Relaxation of KU-1 silica glass structure under annealing

The relaxation process of the KU-1 silica glass structure under annealing at 825–980°C was researched, and the energy of activation of the relaxation process was defined. The formula for calculation of the relaxation time of the KU-1 silica glass is τ = 2 × 10⁻¹⁵ exp(85800/RT), [hour].     

Catalytic vapor-phase oxidation of 2,2,2-trifluoroethanol

The synthesis of trifluoroacetaldehyde by vapor-phase oxidation of 2,2,2-trifluoroethanol using supported vanadium catalysts was studied. Significant differences were observed in the reaction outcomes resulting from different types of catalysts. The ZrO₂- and Al₂O₃-supported catalyst demonstrated both high catalytic activity and selectivity. The addition of co-catalysts such as MoO₃ or SnO₂ improved catalytic performance (Selectivity: up to 91%; S.T.Y.: >200 g L⁻¹ h⁻¹). The experimental results on catalyst lifetime showed a marked decrease in the activity of the Al₂O₃-supported catalyst within tens of hours, while the ZrO₂-supported catalyst showed little, if any, performance alterations for 2000 h.     

Development of a membrane-based vapor-phase bioreactor

A vapor-phase bioreactor has been developed utilizing porous metal membranes in a cylindrical design employing radial flow as opposed to traditional axial flow for the vapor stream. The system was evaluated for the biodegradation ofp-xylene (p-xylene) from a water-saturated air stream byPseudomonas putida ATCC 23973 immobilized onto sand. The biocatalyst was placed in the annular space between two cylindrical, porous stainless-steel membranes. Details of the reactor system are presented along with biological data verifying system performance. The feed flow rate andp-xylene concentration were varied between 60 and 130 cm³/min and 15–150 ppm, respectively. Continuous reactor operation was maintained for 80–200 h with removal efficiencies (based onp-xylene disappearance) between 80 and 95%. The effluent concentration histories were compared to determine the operating range of the bioreactor.     

Stochastic molecular optimization using generalized simulated annealing

We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H₂O and H₂O₃) and to polypeptides. The results obtained for H₂O and H₂O₃ using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable α-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an α-helix structure. We obtain this structure simulating all Φ, Ψ pairs using only a few steps, as compared with conventional methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 647–657, 1998