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.     

Calculation of the molecular exchanging energy of binary surfactants system on the surface monolayer of aqueous solution

By using the binary anionic/cationic surfactants system CH3(CH2)nOSO_3/CH3(CH2)nN (CH3)3 as an ex-ample, the molecular exchanging energy (ε) of adsorption on the surface monolayer of aqueous solu-tion has been studied. ε can be obtained with two methods. One is from the relationship between ε and the molecule interaction parameter (β). This relationship is founded by considering that the adsorption of mixed surfactants on the surface monolayer of solution satisfies the dimensional crystal model condition under which β can be obtained by testing the surface tension of solution. The other is directly from the molecular structure of surfactants with the Lennard-Jones formula. The results for the studied system show that these two methods coincide well.     

Crystal packing and charge transport in single crystals of chrysene derivatives: Impact of halogenation

Crystal packing has strong influence on the charge mobility for organic semiconductors, so the elucidation of the structure-property relationship is important for the design of high-performance organic semiconductors. Halogen substitution has been shown to be a promising strategy to alter the crystal structure without significantly changing the molecular size in previous reports. This paper studies the influence of halogenation on charge transport in single crystals of chrysene derivatives from a theoretical standpoint. The structure-property relationship is first rationalized by investigating the reorganization energy and electronic coupling from the density functional theory calculations. Based on the Marcus charge transfer theory, the mobilities in the molecular monolayer are then calculated with the random walk simulation technique from which the angular resolution anisotropic mobilities are obtained on the fly. It is shown that the mobilities become much larger for holes than those for electrons in the molecular monolayer when the halogenation occurs. Furthermore, the intra-layer charge transport is little influenced by the inter-layer pathways in the single crystals of the halogenated chrysene derivatives, while the opposite case is shown for the crystal of the nonhalogenated chrysene derivative. The reason for the variations of charge transport is discussed theoretically.     

Prediction of semiconducting SiP_2 monolayer with negative Possion's ratio,ultrahigh carrier mobility and CO_2 capture ability

Using particle swarm optimization(PSO) methodology for crystal structure prediction,we predicted a novel two-dimensional(2 D) monolayer of silicide diphosphorus compound:SiP_2,which exhibits good stability as examined via cohesive energy,mechanical criteria,molecular dynamics simulation and all positive phonon spectrum,respectively.The SiP_2 monolayer is an indirect semiconductor with the band gap as 1.8484 eV(PBE) or 2.681 eV(HSE06),which makes it more advantageous for high-frequencyresponse optoelectronic materials.Moreover,the monolayer is a relatively hard auxetic material with negative Possion's ratios,and also possesses a ultrahigh carrier mobility(1.069 × 10~5 cm~2 V~1 s~1) which is approximately four times the maximum value in phosphorene and comparable to the value of graphene and CP monolayers.Furthermore,the effects of strains on band structures and optical properties of SiP2 monolayer have been studied,as well as CO_2 molecules can be strongly chemically adsorbed on the SiP_2 monolayer.A semiconductor-to-metal transition for-9.5% strain ratio case and a huge optical absorption capacity on the order of 106 cm ~1 in visible region present.These theoretical findings endow SiP2 Monolayer to be a novel 2 D material holding great promises for applications in highperformance electronics,optoelectronics,mechanics and CO_2 capturing material.     

Organic interfacial engineering of gold nanowires for selective glycerol electrooxidation

The selective electrochemical conversion of glycerol into value-added products is a green and sustainable strategy for the biomass utilization. In this work, Au nanowires(Au-NW) modified with polyethyleneimine(PEI) molecule(Au-NW@PEI) is obtained by an up-bottom post-modification approach.Physical characterization, molecular dynamics simulation and density functional theory demonstrate that the loose-packed PEI monolayer firmly and uniformly distribute on the Au-NW surface due to the strong Au-N...     

Molecular simulation of alkyl monolayers on the Si(111) surface YUAN

The preparation of monolayers on silicon surface is of growing interest for potential applica-tions in biosensor or semiconductor technology[1—5]. The alkyl modified Si(111) surfaces[6—10] can be obtained using the thermal, catalyzed, or photochemical reaction of hydrogen-terminated sili-con with alkenes, Grignard reagents, and so on. At the same time, the monolayer properties on Si(111) surface have been studied by a variety of experimental methods[8—10] such as X-ray photo-electron spect…     

异丁烯在不同硅铝比的NanZSM-5型分子筛中的吸附：分子模拟研究

Frameworks of NanZSM-5 type zeolites with various Si/A1 ratios have been constructed and optimized with molecular dynamic quench simulation. The results show that the structure parameters of NanZSM-5 type zeolite, including the bond length and atomic charges, are consistent with those predicted by ab initio cluster calculations. It was also observed that atomic charges of Si atoms were shifted to higher field in NanZSM-5 type zeolite with lower Si/Al ratio. Then, the adsorption of isobutene on NanZSM-5 with various Si/Al ratios has been investigated using grand canonical ensemble Monte Carlo simulation and Cvff-300-1.01 forcefield. The simulated adsorption amount was in good agreement with the experimental data. Based on these facts, the effects of Si/Al ratio on the adsorption amount and adsorption isotherms of isobutene on NanZSM-5 were predicted. The results indicated that Si/Al ratio was important for the adsorption of isobutene and the adsorption amount was decreased as the Si/Al ratio was increased, which can be explained that the atomic charge of Na^＋ cation would influence greatly the π electrons of the isobutene double bond due to the Coulomb force. In addition, the adsorption sites of isobutene and interaction energy of isobutene with NanZSM-5 were also discussed.     

Nanofriction properties of molecular deposition films

The nanofriction properties of Au substrate and monolayer molecular deposition film and multilayer molecular deposition films on Au substrate and the molecular deposition films modified with alkyl-terminal molecule have been investigated by using an atomic force microscope. It is concluded that ( i ) the deposition of molecular deposition films on Au substrate and the modification of alkyl-terminal molecule to the molecular deposition films can reduce the frictional force; (ii) the molecular deposition films with the same terminal exhibit similar nanofriction properties, which has nothing to do with the molecular chain-length and the layer number; (iii) the unstable nanofriction properties of molecular deposition films are contributed to the active terminal of the molecular deposition film, which can be eliminated by decorating the active molecular deposition film with alkyl-terminal molecule, moreover, the decoration of alkyl-terminal molecule can lower the frictional force conspicuously; (iv) the relat     

Studies on the Adsorption of Asymmetrical Triblock Copolymers by Scheutjens-Fleer Theory and Monte Carlo Simulation

The adsorption of asymmetrical triblock copolymers from a non-selective solvent on solid surface has been studied by using Scheutjens-Fleer mean-field theory and Monte Carlo simulation method on lattice model. The main aim of this paper is to provide detailed computer simulation data, taking A8-kB20Ak as a key example, to study the influence of the structure of copolymer on adsorption behavior and make a comparison between MC and SF results. The simulated results show that the size distribution of various configurations and density-profile are dependent on molecular structure and adsorption energy. The molecular structure will lead to diversity of adsorption behavior. This discrepancy between different structures would be enlarged for the surface coverage and adsorption amount with increasing of the adsorption energy. The surface coverage and the adsorption amount as well as the bound fraction will become larger as symmetry of the molecular structure becomes gradually worse. The adsorption layer becomes thicker with increasing of symmetry of the molecule when adsorption energy is smaller but it becomes thinner when adsorption energy is higher. It is shown that SF theory can reproduce the adsorption behavior of asymmetrical triblock copolymers. However, systematic discrepancy between the theory and simulation still exists.The approximations inherited in the mean-filed theory such as random mixing and the allowance of direct back folding may be responsible for those deviations.     

Formation Sites and Microscopic Conformation Study on the Konjac Glucomannan Molecular Helices

<正>In this work,the formation sites,helical parameters and hydrogen bond positions of Konjac glucomannan molecular helices were investigated using molecular dynamic simulation method.To our interest,the KGM chain is mainly composed by local left and right helix structures. The formation sites of KGM chain might locate at the chain-segments containing acetyl groups,and the left helix is the favorable conformation of KGM.Temperature-dependent molecule conformation study indicates that the right helix is dominant when the temperature is lower than 343 K,above which,however,the left helix is dominating(right helix disappears).In addition,intramolecular hydrogen bonds in the left helix can be found at the-OH groups on C(2),C(4)and C(6)of mannose residues;comparably,the intramolecular hydrogen bonds in the right helix can be mainly observed at the-OH groups on C(4)and C(6)of the mannose residues and C(3)of the glucose residues.In conclusion,molecular dynamic simulation is an efficient method for the microscopic conformation study of glucomannan molecular helices.     

CONFIGURATION-DEPENDENT PROPERTIES OF POLY(DIMETHYLSILOXANE) CHAIN*

The intermolecular rotational potential energies for poly(dimethylsiloxane) (PDMS) chains aredirectly obtained from a priori probability P_(αβ). Here the differing statistical weight matrices for the Si-Oand O-Si bonds are considered in calculating the configuration partition function. In the Bahar's model, asthe same statistical weight matrices for the Si -O and O- Si bonds are adopted, there exists a large deviationof αpriori probability P_(αβ) between the theory and the molecular dynamics (MD) simulation. Our model givessatisfactory agreement with experiment on the mean-square unperturbed end-to-end distance, the mean-square dipole moment and its temperature dependence, and the molar cyclization equilibrium constants fordimethylsiloxane oligomers. This new rotational isomeric state approach can be widely applied to otherchains, such as -CH_2-C[(CH_2)_mH]_2- and -O-Si[(CH_2)_mH]_2 for arbitrary m.     

Size Effects for the Adsorption of Alkali Metal Atoms on the Si(001) Surface

The adsorptions of a series of alkali metal(AM) atoms, Li, Na, K, Rb and Cs, on a Si(001)-2×2 surface at 0.25 monolayer coverage have been investigated systematically by means of density functional theory calculations. The effects of the size of AM atoms on the Si(001) surface are focused in the present work by examining the most stable adsorption site, diffusion path, band structure, charge transfer, and the change of work function for different adsorbates. Our results suggest that, when the interactions among AM atoms are neglectable, these AM atoms can be divided into three classes. For Li and Na atoms, they show unique site preferences, and correspond to the strongest and weakest AM–Si interactions, respectively. In particular, the band structure calculation indicates that the nature of Li–Si interaction differs significantly from others. For the adsorptions of other AM atoms with larger size(namely, K, Rb and Cs), the similarities in the atomic and electronic structures are observed, implying that the atom size has little influence on the adsorption behavior for these large AM atoms on the Si(001) surface.     

Molecular modeling of epsilon RNA from hepatitis B virus

An initial model of the HBV epsilon RNA was built by the Biopolymer module of InsightⅡ.While its three-dimensional structure was obtained through structure optimization based on molecular dynamics simulation,the two active sites were found.A comparison with the experimental result indicated that the active sites may be the binding sites of the epsilon RNA in the RT-epsilon interaction.The result will be helpful to further discussion about the mechanism of RT-epsilon interaction and the study of HBV genom...     

Ordered supramolecular assembly of bis[3,4,12,13,21,22,30,31-octa(dodecylthio)-2,3-naphthalocyaninato]erbium at the air/water interface

The supramolecular assembly of bis[3, 4, 12, 13, 21, 22, 30, 31-octa(dodecylthio)-2, 3-naphthalocyaninato] erbium complex (Er[Nc(SC12H25)8]2) was fabricated at the air/water interface by Langmuir monolayer technique. Surface pressure-area isotherm indicates that stable monolayer is formed. The monolayer morphology on mica was investigated by atomic force microscopy (AFM). Columnar domains of ca. 100 nm ×(20-30) nm appearing in the micrograph have ordered orientation. Polarized UV-vis spectra and small-angle X-ray diffraction pattern show that the macrocycles tilt in the monolayer. The orientation angle of the naphthalocyanine ring with respect to the substrate was found to be ca. 54°. Each monolayer is ca. 3.53 nm thick. The columnar domain comprises 4-6 rows of columnar supramolecular assemblies where the molecules stack face-to-face.     

Theory and algorithms for the excited states of large molecules and molecular aggregates

This project aims to attack the frontiers of electronic structure calculations on the excited states of large molecules and molecular aggregates by developing novel theoretical and computational methods. The methodology development is especially based on the time-dependent density functional theory (TDDFT) and valence bond (VB) theory, and is expected to be computationally effective and accurate as well. Research works on the following related subjects will be performed: (1) The analytical energy-derivative approaches for electronically excited state within TDDFT will be developed to reduce bypass the computational costs in the calculation of molecular excited-state properties. (2) The ab initio methods for electronically excited state based on VB theory and hybrid TDDFT-VB method will be developed to overcome the limitations of current TDDFT in simulating photophysics and photochemistry. (3) For larger aggregates, neither ab initio methods nor TDDFT is applicable. We intend to build the effective model Hamiltonian by developing novel theoretical and computational methods to calculate the involved microscopic physical parameters from the first-principles methods. The constructed effective Hamiltonian is then used to describe the excitonic states and excitonic dynamics of the natural or artificial photosynthesized systems, organic or inorganic photovoltaic cell. (4) The condensed phase environment is taken into account by combining the developed theories and algorithms based on TDDFT and VB with the polarizable continuum solvent models (PCM), molecular mechanism (MM), classical electrodynamics (ED) or molecular dynamics (MD) theory. (5) Highly efficient software packages will be designed and developed.     

MOLECULAR DYNAMICS SIMULATION ON VIERATIONAL SPECTROSCOPIC FEATURES OF HYDROGEN BONDS IN CRYSTALLINE POLYMERS

Introduction The molecular dynamics simulation technique has recently proved to be a suitable alternative approachfor simulation of vibrational spectroscopy. In this study, molecular dynamics was utilized to understandlow frequency vibrations in highly ordered poly(ρ-phenylene terephthalmide) (PPTA). A key structuralfeature of this polymer is the presence of hydrogen bonds. There is little question that this strong localized     

Unexpected Carrier Mobility Anisotropy in the Two-dimensional Ca_2Si Monolayer from First-principles Calculations

Development of the nano-electronics requires materials with both high carrier mobility and a sufficiently large electronic band gap. In this work, by means of ab initio calculations, we have predicted a new 2D Ca_2Si monolayer with a quasi-planar hexa-coordinate structure. The geometrical structure, stability and electronic properties of Ca_2Si monolayer have been systemically investigated. The Ca_2Si monolayer is an indirect semiconductor with band gap of about 0.77 eV, which exhibits stable chemical bonding interactions as well as thermal and dynamic stability. Moreover, the carrier mobility in Ca_2Si monolayer is electron dominated with a high electron mobility about 4590.47 cm~2×V~(-1)×s~(-1). It is excited that the 2D Ca_2Si monolayer exhibits strong directionally anisotropic carrier mobility, which could effectively facilitate the migration and separation of the generated electron-hole pairs. Our calculations demonstrate that the 2D Ca_2Si monolayer is potential for high efficiency solar cells and other nano-electronic applications.     

Insight into the Urea Binding and K166R Mutation Stabilizing Mechanism of TIpB： Molecular Dynamics and Principal Component Analysis Study

Chemoreceptor TlpB（Tlp=transducer-like protein）, which has been demonstrated to respond to pH sensing function, is crucial for the survival ofHelicobacterpylori（H, pylori） in host stomach. Urea was proposed to be essen- tial for TlpB＇s pH sensing function via binding with the Per-ARNT-Sim（PAS） domain of TlpB. Additionally, KI66R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Al- though X-ray crystallographic studies have been carried out for urea-bound Tlpl3, the molecular mechanism for the stabilization of TIpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis（PCA） for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Aspll4, which were induced by both urea binding and K166R mutation of TIpB, were im- portant to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may Dave the wav for the further researches of TlpB.     

ELASTICITY OF MONOLAYER OF LINOLEIC ACID AND ITS POLYMER

The dynamic elasticity of linoleic acid monolayer on a subphase of10~(-4)mol/L TbCl_3 at various surface pressure has been measured by means of dynamic oscil-lation method in measuring the change of surface pressure caused by periodic compression-expansion cycles of the barrier. The elasticity of monolayer increases with increasing ofsurface pressure linearly. The linoleic acid polymer monolayer has been obtained underUV-irradiation in situ when keeping a constant surface pressure. But the elasticity of theresulting polymerized monolayer is even smaller than that of its corresponding monomermonolayer. The elasticity of the polymerized linoleic acid monolayer decreases with in-creasing polymerization time. The explanation based on entropy has been presented.     

CONTROLLED SYNTHESIS OF AMPHIPHILIC BLOCK POLYMERS HAVING GLUCOSE RESIDUES AND THEIR STRUCTURE FORMATION

Vinyl ether (VE)-based amphiphilic block copolymers with D-glucose residues as hydrophilicpendants were synthesized by CH_3 CH(OiBu)Cl/ZnI_2-initiated sequential living cationic copolymerization of3-O-(vinyloxy)ethyl-1, 2:5, 6-di-O-isopropylidene-D-glucofuranose (IGVE) and isobutyl VE (IBVE ) andsubsequent deprotection. The precursor block copolymers had a narrow molecular weight distribution(M_w/M_n～1.1) and a controlled segmental composition. The solubility characteristics of the amphiphiliccopolymer depended strongly on composition. Their solvent-cast thin films were examined, under atransmission electron microscope, and could be seen to exhibit various microphase-separated surfacemorphologies such as spheres, cylinders, and lamellae, depending on composition. The amphiphiliccopolymers with the appropriate segmental composition were found to form a stable monolayer at the air-water interface, which was successfully transferred onto a substrate by the Langmuir-Blodgett (LB)technique. The layered strucfure of the built-up LB films was controlled by blending the homopolymer.