Hydrogen-bond dynamics of interior and surface molecules in a water nanocluster: temperature and size effects

Molecular dynamics simulations are employed to investigate the effects of temperature and size on the hydrogen-bond dynamics of interior molecules and surface molecules in a water nanocluster. The flexible three-centred (F3C) water model is invoked in the simulations. To inspect the dynamics of the interior hydrogen bonds and the surface hydrogen bonds, a spherical water nanocluster is modelled and then divided into interior molecules and surface molecules according to the density profile of the water nanocluster. It is observed that at higher temperatures the average number of hydrogen bonds decreases and yields faster hydrogen-bond relaxation for both interior molecules and surface molecules of the water nanocluster. Furthermore, the surface molecules have a lower average number of hydrogen bonds than the interior molecules. The lifetime of the surface hydrogen bonds is slightly longer than that of the interior hydrogen bonds, whereas the hydrogen-bond structural relaxation time of the surface molecules is more obviously slower than that of the interior molecules. Regarding the size effect, a larger water nanocluster is seen to have a larger average number of hydrogen bonds and a longer hydrogen-bond structural relaxation time.     

菌紫质光致各向异性动力学的理论和实验

对菌紫质(Bacteriorhodopsin,BR)薄膜的光致各向异性特性进行了理论模拟.由随机取向的极性BR分子构成的聚合物薄膜在宏观上是各向同性的,但在线偏振光的作用下,BR分子对激发光的选择性吸收,导致不同异构体分子取向的不均匀分布,从而使BR薄膜在宏观上呈现出各向异性.利用BR光循环的二能级模型,得到了B态分子取向分布随时间的变化关系,推导出了BR薄膜光致各向异性动力学的数学表达式,模拟了不同激发光强下BR薄膜的光致各向异性动力学曲线,得到了和实验结果一致的计算结果.     

Molecular mechanism of gelation with ethylene glycol added to a solution of polyacrylonitrile in dimethylsulfoxide

The mechanism of solidifying a solution of polyacrylonitrile (PAN) in dimethylsulfoxide (DMSO) into which ethylene glycol is added is studied by the method of Raman spectroscopy. In the absence of ethylene glycol, DMSO molecules produce dipole-dipole bonds to PAN molecules. Upon adding ethylene glycol, DMSO molecules form hydrogen bonds with it and a line at 1000 cm⁻¹ appears in the Raman spectrum, which is assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. After DMSO is removed, ethylene glycol molecules produce hydrogen bonds with two neighboring PAN molecules, giving rise to a band at 2264 cm⁻¹, which is assigned to the valence vibrations of C≡N bonds involved in these hydrogen bonds. A high-viscosity gel consisting of PAN molecules arises in which these molecules are bonded to each other through ethylene glycol molecules.     

Initial stage of adsorption of octithiophene molecules on Cu(111)

The initial stage of the adsorption of octithiophene (8T) molecules on a Cu(111) surface is investigated using a scanning tunneling microscope at room temperature. We find a characteristic molecular chain structure of 8T molecules on a terrace of the Cu(111) surface, which has not been reported so far for adsorption of oligothiophene molecules on metal surfaces. Up to the adsorption of 0.26 monolayer (ML), 8T molecules in the molecular chain align with their long axis parallel to the Cu<11-2> direction. With increasing coverage, there appear 8T molecules that align with their long axis parallel to the Cu<110> direction. The appearance of different molecular orientations is understood by the decrease of the number of the adsorption sites for extending the molecular chains. Fragments of 8T molecules, such as single thiophene molecules, are also observed in this work. They are trapped only at the step edges of the Cu(111) surface at the beginning and later trapped in a small Cu(111) region surrounded by 8T molecules.     

醇类抑制剂对甲烷水合物形成的影响

在本工作中,甲烷水合物的生长动力学是通过甲醇、乙醇、乙二醇三种不同醇类抑制剂存在下的分子动力学模拟研究的.模拟结果发现,三种醇类都可作为甲烷水合物的抑制剂,醇类分子中的亲水性羟基极大地破坏了水合物笼的结构,并且羟基可以与局部的液态水分子形成氢键,从而增加了形成水合物笼型结构的难度,导致甲烷水合物的生长速率降低.对于甲醇分子,甲醇分子的亲水性羟基与水分子形成氢键从而破坏了水分子结构,而亲油性甲基对周围的水分子具有簇效应,两者都会降低水合物生长速率;对于乙二醇和乙醇分子,它们只含有羟基,特别是乙二醇分子含有两个羟基,其对H₂O分子有很强的吸附作用,导致水合物生长速率降低.在抑制效果方面,甲醇分子最优,乙二醇稍微优于乙醇.     

Solutions of novel soliton molecules and their interactions of (2 + 1)-dimensional potential Boiti-Leon-Manna-Pempinelli equation

The method of variable separation has always been regarded as a crucial method for solving nonlinear evolution equations. In this paper, we use a new form of variable separation to study novel soliton molecules and their interactions in (2+1)-dimensional potential Boiti-Leon-Manna-Pempinelli equation. Dromion molecules, ring molecules, lump molecules, multi-instantaneous molecules, and their interactions are obtained. Then we draw corresponding images with maple software to study their dynamic behavior.     

Adiabatic similarity and dependence of the energy of molecular systems on the masses of particles

The dependence of the energy of three-particle molecules on their masses is examined. It is shown that such molecules with the same values of the ratio of the reduced masses for motion in a “fast” and “slow” Jacobi coordinates have the property of adiabatic similarity: In the adiabatic approximation, their energies are proportional to the reduced masses. This allows information on the energy of molecules symmetric in the masses of particles to be extended to asymmetric molecules adiabatically similar to the symmetric molecules. For molecules with arbitrary masses of the particles, an analytic expression for the adiabatic energy and a formula approximating the exact energy are constructed using the principle of adiabatic similarity. Along with the adiabatic energy, which is the lower bound of the exact energy, a simple procedure is considered for determining the upper bound of the energy of asymmetric molecules from the energy of their symmetric counterparts. Based on these results, values of the lower and upper energy bounds are calculated and an approximation of the exact energy is obtained for 43 three-particle molecular systems.     

荧光法研究几种分子在海藻酸钙空心胶囊中的缓释性能

实验中选取了带有正电罗丹明6G分子、带有负电荷荧光素分子、中性的尼罗红分子和生物分子R-藻红蛋白为模型分子.将这几种分子分别包封于海藻酸钙窄心胶囊中.实验表明囊芯分子的电性对其在海藻酸钙空心胶囊中缓释性能有影响,带有正电荷罗丹明6G分子的扩散过程中,多孔聚合物骨架扩散是主要过程.中性分子则表现出来一个膜相溶出和多孔聚合物骨架扩散共同控制的过程.带有负电荷荧光素分子,由于静电排斥作用,加剧囊芯分子的运动.从而使得荧光素分子可以直接从膜相溶出.此外.南于胶囊囊壁上带有负电,不论是带有正电荷还足带有负电荷的分子都会延长其达到扩散平衡的时间.而电中性分子由于没有库仑相互作用的影响更容易达到平衡.囊芯和囊辟相互作用强的其扩散系数小,反之其扩散系数大.R-藻红蛋白的扩散完全是一个多孔聚合物骨架扩散控制的过程.由于分子的体积比较大,因此扩散的平衡时间也比较长.     

Modelling of spreading process: effect from hydrogen bonds

Lubricant spreading on solid substrates has drawn considerable attention not only for the microscopic wetting theory but also for the dramatic application in head-disk interface of magnetic storage drive systems. Molecular dynamic simulation based on a coarse-grained bead-spring model has been used to study such a spreading process. The spreading profiles indicate that the hydrogen bonds among lubricant molecules and the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will complicate the spreading process in a tremendous degree. The hydrogen bonds among lubricant molecules will strengthen the lubricant combination intensity, which may hinder most molecules from flowing down to the substrates and diffusing along the substrates. And the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will confine the lubricant molecules around polar atoms, which may hinder the molecules from diffusing along the substrates and cause precursor film to vanish.     

碳纳米胶囊中水分子的分子动力学研究

采用分子动力学方法研究了不同温度下碳纳米胶囊中水分子及其氢键的聚集密度分布,讨论了水分子内部键角及其取向规律.计算结果表明,由于碳纳米胶囊的束缚作用,水分子主要聚集在与胶囊形状相似的三个薄层中,随着温度的升高,聚集密度峰均会展宽并向管壁移动.氢键的分布规律与水分子聚集密度类似并对其取向角分布有明显影响.与通常情况不同,在1000K高温时仍存在相当数量的氢键.在3100 K附近,碳纳米胶囊发生破裂,溢出少量水分子后自动愈合.     

Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.     

药物小分子穿越磷脂双层膜输运过程中的时滞效应

本文基于扩散动力学,建立了一种新的药物小分子穿越磷脂双层膜输运的理论模型,研究药物小分子穿越磷脂双层膜输运的动态过程,考察药物小分子跨膜输运过程中的时间延迟(时滞)效应。研究发现,药物小分子在数分钟内穿越磷脂双层膜各区域进入细胞,由于时滞效应,穿膜过程呈现了周期性演化特性。当药物小分子数量增加到一定程度,磷脂分子层会出现微小孔,让积累的药物小分子快速通过。通过分析模型中各参数的敏感性,我们还发现,药物小分子在磷脂双层膜内不同区域的扩散特性,以及输运过程的时滞性,都会对药物小分子穿越磷脂双层膜的动力学有较大程度的影响。理论结果符合模拟、实验观测,进一步深刻揭示了药物小分子穿越磷脂双层膜的穿膜特性,可为设计确切的疗法药物提供必要的参考和新方案。     

Fabrication of polymer dot pattern containing fluorescent molecules by laser photopolymerization

A simple and easy method for micro-patterning of organic molecules was developed. Fluorescent molecules were added to an ultraviolet (UV) photopolymerization polymer solution, and dot patterns were formed by a photopolymerization process with a conventional nanosecond pulsed UV laser. Since the molecules fixed in the dot pattern showed fluorescence corresponding to the added molecules in all cases, it is suggested that this method is applicable to micro-patterning of various kinds of organic molecules without serious damage to the molecules. Micro-patterning was also achieved using a visible pulsed laser by adding coumarin 6 to the polymer solution.PACS 82.50.Hp; 81.65.Cf; 81.05.Lg     

Conductivity of solutions of poly(acrylonitrile) in dimethyl sulfoxide

The conductivity of solutions of poly(acrylonitrile) (PAN) in dimethyl sulfoxide (DMSO) is studied. Using the Raman spectroscopy method, it is found that PAN causes associates of DMSO molecules to dissociate into free molecules, as a result of which the conductivity of the solution grows. Simultaneously, PAN molecules hamper the rotation of DMSO molecules, which decreases the conductivity. There exists a critical concentration of PAN (≈5.4 vol. %) at which the rotation of DMSO molecules is hindered to the greatest extent and the conductivity drops by an order of magnitude.     

Modeling of the vibrational structure of the vibronic spectra of diphenylpolyenes by the parametric method

The structures of the electronic-vibrational spectra and of the excited states of a number of diphenylpolyene molecules are determined within the framework of the second approximation of the parametric method. The system of parameters of the structural fragments of molecules is improved and good agreement with spectral experiment is obtained. It is shown that there is a high degree of transferability of the polyene and acene parameters of the method and that the models obtained are adequate to the real structure of molecules. It is also shown that the method proposed makes it possible to perform predictive qualitative and quantitative calculations of the spectra of these molecules, as well as of the spectral characteristics necessary for modeling photochemical molecular transformations. In the series of diphenylpolyene molecules, an interpretation of the vibrational structure of the spectra is proposed and the specific features of variation of the geometry upon excitation of molecules are considered.     

Microdot pattern of multiple organic molecules prepared by laser photopolymerization process with a nanosecond pulsed laser

A microdot pattern of multiple organic molecules was prepared. Fluorescent molecules, which absorb visible light, were added to a commercial ultraviolet photopolymerization polymer solution and the polymer solution was polymerized by irradiating with nanosecond pulsed visible laser light. The size and the shape of the polymerized dots differed with the irradiation condition and the kind of the added molecules. Based on these results, a microdot pattern of multiple organic molecules was prepared by repeating a micropatterning process with the molecules. PACS 82.50.Hp; 81.65.Cf; 81.05.Lg     

Electrostatic investigation into the bonding of poly(phenylene) thiols to gold

The advancement of nanotechnology relies on the understanding of electrical connection to individual molecules. Electrostatic surface potential measurements of self-assembled monolayers can provide insight into the structural and electronic properties of molecules attached to surfaces. In this paper we report on the electrostatic potential of poly(phenylene) thiol molecules bound to gold surfaces. Kelvin force microscopy is used to probe self-assembled monolayers of a series of phenyl, biphenyl, and triphenyl thiol molecules. The dipole moments of the isolated molecules have been determined and show similar electronic trends. A difference in polarity between the isolated molecules and the electrostatic surface potential of a monolayer attached to gold reflects the electron transfer on to the bound molecule.     

A Theoretical Study of a Single-Walled ZnO Nanotube as a Sensor for H_2 O Molecules

We have studied the property of single-walled ZnO nanotubes with adsorbed water molecules, and theoretically designed a new sensor for detecting water molecules using single-walled ZnO nanotubes using a combination of density functional theory and the non-equilibrium Green's function method. Details of the geometric structures and adsorption energies of the H 2 O molecules on the ZnO nanotube surface have been investigated. Our computational results demonstrate that the formation of hydrogen bonding between the H 2 O molecules and the ZnO nanotube, and adsorption energies of the H 2 O molecules on the ZnO nanotube are larger than the adsorption energies of other gas molecules present in the atmospheric environment. Moreover, the current-voltage curves of the ZnO nanotube with and without H 2 O molecules adsorbed on its surface are calculated, the results of which showed that the H 2 O molecules form stable adsorption configurations that could lead to the decrease in current. These results suggest that the single-walled ZnO nanotubes are able to detect and monitor the presence of H 2 O molecules by applying bias voltages.     

Alignment of molecules by strong laser pulses

We review how moderately intense laser fields offer an approach to alignment of molecules [1]. In particular, molecules can be aligned along a given space fixed axis, forced to a plane, or their rotations about all three possible axes can be eliminated by choosing a linearly polarized, a circularly polarized, or an elliptically polarized alignment field, respectively. We show how molecules in the gas phase can be aligned by turning on the laser field either slowly (a few nanoseconds) or fast (a few picoseconds) with respect to the rotational period of the molecules. The role of the intensity of the laser field and the rotational temperature of the molecules is discussed. Before concluding we describe how aligned molecules enables control and selectivity in the interaction between polarized light and molecules.Received: 15 November 2002, Published online: 18 March 2003PACS: 33.15.Bh General molecular conformation and symmetry; stereochemistry - 32.80.Lg Mechanical effects of light on atoms, molecules, and ions - 33.80.Gj Diffuse spectra; predissociation, photodissociation - 33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g. Rydberg states) - 34.50.Lf Chemical reactions, energy disposal, and angular distribution, as studied by atomic and molecular beams     

Use of bulk and surface negative ionization to detect laser-excited molecules

The influence of vibrational excitation of molecules on negative-ion formation in bulk and in surface is analyzed. The magnetron method is used to study the influence of laser emission on the formation of negative ions of the molecules SF 6 and 12. The SF 6 molecules were excited by absorption of C02-1aser emission in the v 3 band. The 12 molecules were excited by Stokes scattering of the second harmonic of a neodymium laser. It is shown that the cross section for dissociative capture in the presence of vibrationally excited 12 molecules is increased by 3-4 orders. With SF~ molecules vibrationally excited in the beam, studies were made of the effects of formation of negative ions from a hot polycrystallinetungsten filament. The physics of the influence of vibrational excitation on negative-ion formation on a surface is analyzed. The maximum sensitivities of methods of vibrationally excited molecules are estimated.Translated from Lazernye Sistemy, pp. 121–142 1982.