Investigation of the Adsorption and Self Assembly of Isocyanide Derivatives on Au（111） Surface

The adsorption and self-assembly of isocyanide derivatives on Au（111） surface were investigated by density functional theory （DFF） and molecular dynamics simulation. The calculation for phenyl isocyanide by DFT was based on cluster and slab models. The self-assembled monolayers of 2-isocyanoazulene and 1,3-diethoxycarbony 1- 2-isocyanoazulene on Au（111） were simulated using Au-C force field parameters developed by us. It was found that the top site was the most preferred position, and the isocyanoazulene and its derivatives could form the ordered face to edge self-assembled monolayer on gold surface indeed, and the molecules stood on the gold surface vertically.     

DFT Study of Thiophene Adsorption on the Pd（111） and Pt（111） Surfaces

Thiophene adsorption on the(111) surfaces of Pd and Pt have been investigated by density functional theory.The results indicate that the adsorption at the hollow sites is the most stable.To our interest,the molecular plane of thiophene ring is distorted with C=C bond being elongated to 1.450  and C-C bond being shortened to 1.347 ,and the C-H bonds tilt 13.91～44.05o away from this plane.Furthermore,analysis on population and density of states verified the calculated adsorption geometries.Finally,charge analysis suggests that thiophene molecule is an electron acceptor,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.     

A DFT Study of Thiophene Adsorption on the Rh（111） Surfaces

Thiophene adsorption on the Rh(111) surfaces has been investigated by density functional theory.The results show that the adsorption at the hollow and bridge sites is the most stable.The molecular plane of the thiophene ring is distorted,the C=C bond is stretched to 1.448  and the C-C bond is shortened to 1.390.The C-H bonds tilt 22～42oaway from the surface.The calculated adsorption geometries are in reasonable agreement with population analysis and density of states.The thiophene molecule obtains 0.74 electrons,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.The reaction paths and transition states for desulfurization of the molecule have been investigated.The bridge adsorption structure of thiophene leads to a thiol via an activated reaction with an energetic barrier of 0.30 eV.This second step is slightly difficult,and dissociation into a C4H4 fragment and a sulfur atom is possible,with an energetic barrier of 0.40 eV.     

The Study on the Self-assembled Monolayer （SAMs） of Porphyrin with Different Chain Length by Scanning Electrochemical Microscopy （SECM）

Self-assembled monolayers (SAMs) have become a subject of intense interest in materials science and molecular technologies, because they provided highly ordered structures on the surfaces. SAMs, comprising hydrocarbons bound to the gold surface via a S-Au…     

Density Functional Theory Study on the Adsorption of CN on Transition Metal M（100） （M = Ni,Pd, Pt,Cu, Ag and Au） Surfaces

The adsorption of cyanide on the top site of a series of transition metal M（100） （M = Cu, Ag, Au, Ni, Pd, Pt） surfaces via carbon and nitrogen atoms respectively, with the CN axis perpendicular to the surface, has been studied by means of density functional theory and cluster model. Geometry, adsorption energy and vibrational frequencies have been determined, and the present calculations show that the adsorption of CN through C-end on metal surface is more favorable than that via N-end for the same surface. The vibrational frequencies of CN for C-down configuration on surface are blue-shifted with respect to the free CN, which is contrary to the change of vibrational frequencies when CN is adsorbed by N-down structure. Furthermore, the charge transfer from surface to CN causes the increase of surface work function.     

Effects of Non-specific and Specific Solvation on Adsorption of BPTI on Au Surface： Insight from Molecular Dynamics Simulation

Proteins adsorption at solid surfaces are of paramount important for many natural processes. However, the role of specific water in influencing the adsorption process has not been well understood. We used molecular dynamics simulation to study the adsorption of BPTI on Au surface in three water environments （dielectric constant model, partial and full solvation models）. The result shows that a fast and strong adsorption can occur in the dielectric environment, which leads to significant structure changes, as confirmed by great deviation from the crystal structure, largely spreading along the Au surface, rapid lose in all secondary structures and the great number of atoms in contact with the surface. Compared to the dielectric model, slower adsorption and fewer changes in the calculated properties above are observed in the partial solvation system since the specific water layer weakens the adsorption effects. However, in the partial solvation system, the adsorption of polar Au surface causes a significant decrease in the specific hydration around the protein, which still results in large structure changes similar to the dielectric system, but with much less adsorption extent. Enough water molecules in the full solvation system could allow the protein to rotate, and to large extent preserve the protein native structure, thus leading to the slowest and weakest adsorption. On the whole, the effects of non-specific and specific solvation on the protein structure and adsorption dynamics are significantly different, highlighting the importance of the specific water molecule in the protein adsorption.     

The Effect of Boron on the Properties of Glucomannan： An Experimental and Molecular Dynamics Simulation Study

1 INTRODUCTION gel using KGM and borax at 60 ℃, which can be used as slow-released reagent of theophylline and Generally, the mixture of Konjac Glucomanan dibucaine. And Hogi Tsuneo utilized KGM and tetra- (KGM) and salts that could be hydrolyzed to form valent boric acid to prepare artificial crystal[1]. This multi-hydroxyl hydrates leads to the generation of kind of crystal has good light transmission property, gelatum. Among the familiar salts, such as borate, elasticity, intensi…     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

A Periodic Density Functional Study on Adsorption Properties of Methoxy on Au（111） Surface

1INTRODUCTION Methoxy(CH3O)has been identified as the first intermediate in the decomposition of methanol on extensive list of clean transition metal surfaces,such as Ni(100)[1],Cu(100)[2,3],Cu(111)[4],Ag(111)[5],Au(110)[6],Pd(111)[7]and Ru(0001)[8].The electronic structure of the metal is a determining factor in OH bond scission.In fact,group IB clean surfaces have shown very low activity towards this reaction,al-though there are reports on low amounts of methoxy formed on clean Cu(…     

Theoretical Studies on the Binding of Cd~（2＋） to Uracil and Its Thio-derivatives

The interaction of Cd2+ with uracil,2-thiouracil,4-thiouracil and 2,4-dithiouracil have been investigated by the density functional theory(DFT) calculations.For uracil and 2,4-dithiouracil,where the two basic sites are the same,Cd2+ attachment to the heteroatom at position 4 is preferred.However,for the systems where both types of basic centers,a carbonyl and a thiocarbonyl groups,are present,Cd2+ association with sulfur is favorable.The enhanced stability of these enolic and thiol forms comes from Cd2+ interaction with two basic sites simultaneously,which thereby triggers a significant aromatization of the ring.More significantly,the Cd2+ binding energy with uracil and its thio-derivatives is larger than the tautomerization barriers connecting the diketo-like forms with the corresponding enolic-like tautomers.Consequently,when associated with Cd2+,all tautomers are energetically accessible and should be observed in the gas phase.     

Intermixed Adatom and Surface‐Bound Adsorbates in Regular Self‐Assembled Monolayers of Racemic 2‐Butanethiol on Au(111)

In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self‐assembled monolayer (SAM) of racemic 2‐butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom‐bound motifs plus two RS species bound directly to face‐centered‐cubic and hexagonally close‐packed sites. This is the first time that these competing head‐group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30 %), much larger than that for enantiomerically resolved 2‐butanethiol or secondary‐branched butanethiol (25 %) and near that for linear‐chain 1‐butanethiol (33 %).     

Self-assembled Monolayers of n-Hexadecanoic Acid and α-Hydroxyl n-Hexadecanoic Acid on Titanium Surfaces

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电势诱导的N-异丁酰基-L-半胱氨酸分子在金(111)表面的相转变

Functional solid substrates modified by self-assembled monolayers (SAMs) have potential applications in biosensors, chromatography, and biocompatible materials. The potential-induced phase transition of N-isobutyryl-L-cysteine (L-NIBC) SAMs on Au (111) surfaces was investigated by in-situ electrochemical scanning tunneling microscopy (EC-STM) in 0.1 mol·L^-1 H₂SO₄ solution. The NIBC SAMs with two distinct structures (α phase and β phase) can be prepared by immersing the Au (111) substrate in pure NIBC aqueous solution and NIBC solution controlled by phosphate buffer at pH 7, respectively. The as-prepared α phase and β phase of NIBC SAMs show various structural changes under the control of electrochemical potentials of the Au (111) in H₂SO₄ solution. The α phase NIBC SAMs exhibit structural changes from ordered to disordered structures with potential changes from 0.7 V (vs saturated calomel electrode, SCE) to 0.2 V. However, the β phase NIBC SAMs undergo structural changes from disordered structures (E < 0.3 V) to γ phase (0.4 V < E < 0.5 V) and finally to the β phase (0.5 V < E < 0.7 V). EC-STM images also indicate that the phase transition from the β phase NIBC SAMs to the α phase occurs at positive potential. Combined with density functional theory (DFT) calculations, the phase transition from the β phase to the α phase is explained by the potential-induced break of bonding interactions between ——COO^- and the negatively charged gold surfaces.     

Self‐assembled Monolayers of Alkylphosphonic Acids on Aluminum Oxide Surfaces – A Theoretical Study

Density‐functional based calculations were used to investigate self‐assembled monolayers of different alkylphosphonic acids on corundum α‐Al₂O₃ (0001), bayerite β‐Al(OH)₃ (001) and boehmite γ‐AlOOH (010) surface models. Mono‐, bi‐, and tridentate adsorption modes were considered. In addition, the organization of single adsorbed molecules was compared to the organization at full surface coverage. The height (thickness) of the self‐assembled monolayers is always shorter than the length of the phosphonic acid molecules due to tilting of the alkyl chains. Tilt angles at full surface coverage are very similar to the tilt angle of a single adsorbed molecule, which indicates that the density of the self‐assembled monolayers is limited by the density of adsorption sites. The lateral interactions between alkyl chains are evidenced by small torsions of the adsorbed molecules, which may serve to minimize the repulsion forces between interchain hydrogen atoms. Similar tilt angles were obtained for mono‐, bi‐, and tridentate adsorptions. Hence, the coordination mode cannot be characterized by the molecule tilting.     

Molecular Simulation study of Alkyl Monolayers on Si(III) Surface

The preparation of monolayers on silicon surface is of growing interest for potential applications in biosensor or semiconductor technology. Different experimental technique can be used to investigate the alkyl modified Si(III) surfaces1-4, such as X-ray photoelectron spectroscopy (XPS), Fourier transform infrared absorption spectra(FTIR), scanning electron microscopy (SEM), Auger electron spectroscopy (AES), scanning tunneling microscope (STM), and so on. These experimental results…     

分子动力学与第一原理研究二氧化铈(CeO2)n (n=1～5)纳米粒子的结构性质

二氧化铈纳米粒子(CeO2)n(n=1～5)材料为固态氧化燃料电池中的催化剂,因此了解其不同尺寸结构的性质是非常重要的.在本论文中使用分子动力学(molecular dynamics)模拟结合火焰算法(FIRE algorithm)计算得到二氧化铈的最小能量结构.再应用密度泛函理论方法(density functional theory)对这些结构进一步计算,得到更精确的最低能量结构.     

Observation of Collective Photoswitching in Free‐Standing TATA‐Based Azobenzenes on Au(111)

Light‐induced transitions between the trans and cis isomer of triazatriangulenium‐based azobenzene derivatives on Au(111) surfaces were observed directly by scanning tunneling microscopy, allowing atomic‐scale studies of the photoisomerization kinetics. Although the azobenzene units in these adlayers are free‐standing and spaced at uniform distances of 1.26 nm, their photoswitching depends on the isomeric state of the surrounding molecules and, specifically, is accelerated by neighboring cis isomers. These collective effects are supported by ab initio calculations indicating that the electronic excitation preferably localizes on the n–π* state of trans isomers with neighboring cis azobenzenes.