Dependence of single-molecule conductance on molecule junction symmetry

The symmetry of a molecule junction has been shown to play a significant role in determining the conductance of the molecule, but the details of how conductance changes with symmetry have heretofore been unknown. Herein, we investigate a naphthalenedithiol single-molecule system in which sulfur atoms from the molecule are anchored to two facing gold electrodes. In the studied system, the highest single-molecule conductance, for a molecule junction of 1,4-symmetry, is 110 times larger than the lowest single-molecule conductance, for a molecule junction of 2,7-symmetry. We demonstrate clearly that the measured dependence of molecule junction symmetry for single-molecule junctions agrees with theoretical predictions.     

Electron Transport through Single π‐Conjugated Molecules Bridging between Metal Electrodes

Understanding electron transport through a single molecule bridging between metal electrodes is a central issue in the field of molecular electronics. This review covers the fabrication and electron‐transport properties of single π‐conjugated molecule junctions, which include benzene, fullerene, and π‐stacked molecules. The metal/molecule interface plays a decisive role in determining the stability and conductivity of single‐molecule junctions. The effect of the metal–molecule contact on the conductance of the single π‐conjugated molecule junction is reviewed. The characterization of the single benzene molecule junction is also discussed using inelastic electron tunneling spectroscopy and shot noise. Finally, electron transport through the π‐stacked system using π‐stacked aromatic molecules enclosed within self‐assembled coordination cages is reviewed. The electron transport in the π‐stacked systems is found to be efficient at the single‐molecule level, thus providing insight into the design of conductive materials.     

单分子毛细管电泳

对室温下液流中的单分子光学检测技术的基本原理、主要方法以及它在生物学中的应用做了综述。重点强调了毛细管电泳与单分子检测相结合-单分子毛细管电泳在分析科学中战略上的重要性，并展望了单分子光学检测技术为特征的单分子毛细管电泳在分析化学中的应用前景。     

Intensity enhancement of the vibrational spectrum of oxygen when attached to a platinum nanocluster

Detecting single molecules is a technical and scientific challenge and requires to increase the number of molecules or their cross section to a radiation field in order to have a detectable signal. We demonstrate for a single molecule of oxygen that, by attaching the molecule to a nanocluster, the molecule signature spectrum is transferred to the larger complex (molecule cluster). Therefore, the detection can focus on the complex, which can have a much larger cross section, rather than on the small molecule. This is based on the concept of signature transfer, which can be used to detect in the cluster several other properties of the attached molecule.     

Evaluation of effect of functionalized gold nanoparticles with a partial negative charge on stability of DNA molecule: a study of molecular dynamics simulation

Today, understanding the interaction between DNA molecule with nanoparticles and functionalized nanoparticles has a significant importance in medical applications and targeted drug delivery. Molecular dynamics simulation on double-stranded molecule with the structure of the double helix and sequence of (CCTCAGGCCTCC) was performed in three states. The aim was to evaluate the effect of gold nanoparticles (GNPs) with partial negative charge on the stability of a DNA molecule. During the simulation process, the GNPs become closed to the DNA molecule and phosphate groups of the DNA molecule guided the nanoparticles toward its major groove. At the end of the DNA molecule chain, the terminal nucleotide of the chain was laid flat on the surface of the GNPs due to excessive exposure to solvent molecules and occurrence of peeling and untwisting states. According to the results, proximity of the GNPs and functionalized GNPs to the DNA molecule led to increased configuration entropy. While conformational energy and van der Waals energy of the DNA molecule increased in the presence of the GNPs and functionalized GNPs, there was a reduction and an increase in the number of hydrogen bonds between complementary bases in the presence of the GNPs and functionalized GNPs, respectively. Radial distribution function was estimated for water molecules and sodium cations, compared to oxygen atoms of the phosphate group of the DNA molecule. Results were indicative of the release of water molecules from around the DNA molecule in the presence of the GNPs. In addition, the distance between sodium cations and the GNPs decreased. Nevertheless, no such phenomenon occurred in the presence of the functionalized GNPs. Therefore, according to results, it seems that GNPs decreased the stability of the DNA molecule and the functionalized GNPs with partial negative charge caused structural changes and created compression, but did not destroy the double-strand structure of the DNA molecule.     

Atomistic simulations of an antimicrobial molecule interacting with a model bacterial membrane

The dynamics of an antimicrobial molecule (end-only oligo(p-phenylene ethynylene) or EO-OPE-1 (C3)) interacting with a model bacterial membrane is simulated using all-atom molecular dynamics. It is found that the molecule spontaneously adheres to the membrane at the membrane?Cwater interface, but no insertion into the bilayer was observed within the nanosecond simulation time. However, when the simulations start from an inserted configuration, this molecule aligns with the lipid molecules in the membrane and interacts strongly through electrostatic interactions with the anionic phosphoryl groups of the lipid molecules. Due to the hydrophobic mismatch between the molecule and lipids, the inserted molecule induces the deformation of the membrane in the form of local thinning. When more than one molecule were inserted, self-assembling was observed on a nanosecond scale. However, no transmembrane pore formation was observed, due presumably to the hydrophobic backbone of the molecule. Implications in the biocidal action of this molecule are discussed.     

Concepts of Trapping Topologically by Shell Molecules

Concepts of the synthesis of shell topological compounds, which consist of a guest molecule (or molecules) trapped by a host molecule with a spacial, egg shell-like structure are discussed. Generally, both constructing the shell molecule in the presence of a guest molecule and constructing the guest molecule in the presence of the shell (host) are ways to “shell” topological compounds. The preparation of shell molecules may consist of the completion of “preshell” molecules or of obtaining cascade branched oligomers and polymers. Cyclodextrins and substances like triquinance are considered to play a role in preshell molecules. Shell molecules may also be obtained by polyreaction of a monomer of the XRY_n type, which results in a cascade branched molecule of shell structure (spherical form). When the polyreaction is continued, the cascade branched molecule becomes a “cast” one. It is theoretically possible to enclose a guest molecule inside the shell during the cascade branching process if there is a good solvent (of high expansion coefficient value) in respect to the growing branches. A spacially developed molecule of both “empty” and “cast” structure may be obtained also by the known “step by step” cascade branching process which involves, for instance, a repeated cyanoethylation-reduction reaction.     

电场作用下C60富勒烯二聚体分子的几何构型与失效

By the molecular mechanics/quantum mechanics method, the geometry distortion and configuration invalidity of dimmer C60fullerene (2C60) molecule in external electric field are simulated. The effect of the electric field, with three different directions, on geometry distortion, configuration invalidity, polarization charge distribution and dipole moment for 2C60 molecule is discussed systemtically. Further the geometry distortion and invalidity of 2C60 molecule are respectively compared with those of C60 fullerene molecule in electric field. By comparison, it is shown that geometry distortion and configuration invalidity behavior of 2C60 molecule are sensitive to the direction of electric field, when the directions of the applied electric field are parallel to the bridged C-C bonds. For 2C60molecule it is very easy for the configuration of 2C60 molecule to be invalidated and the invalidity mode is very particular as well.     

单分子酶学研究进展

源于20世纪90年代的单分子显微成像技术成功实现了对单分子酶的催化过程实时监控,此后单分子酶学的研究进入了快速的发展时期,发现了多种酶的新单分子行为及反应机制。单分子酶学的研究能够发现隐藏于整体平均水平下的单个酶分子的个体行为,揭示了酶与底物作用的动态变化,加深了人们对各种生化反应的理解。     

5,6]-Heterofullerene-like C58Ge: odd atoms assembling a cage

Density functional calculations and structural minimization techniques have been employed to characterize the structural and electronic properties of [5,6]-heterofullerene-like C(58)Ge. The heterofullerene molecule has an odd number of atoms on the skeleton of the cage and is a novel molecule. The vibrational frequencies of the molecule have been calculated at the B3LYP/3-21G level of theory. The absence of imaginary vibrational frequency confirms that the molecule corresponds to a true minimum on the potential energy hypersurface. Its heat of formation was estimated in this study. Since the symmetry of the molecule of [5,6]-heterofullerene-like C(58)Ge is C(2), it is a chiral molecule.     

Elucidating the mechanism of binding of chromate to cucurbit[6]uril: a DFT study

We report the binding of chromate, a toxic heavy metal ion to the macrocyclic host molecule, cucurbituril using density functional theory. Due to the anionic nature of the guest molecule and the portals of the host molecule, we propose that the binding mechanism should be assisted by cations. The calculated barrier for chromate binding to cucurbituril is found to be?~17?kcal?mol^?1. The large barrier can be attributed to portal opening of the host molecule, electrostatic repulsion between the guest molecule and the portals of the host molecule and the solvent re-organization around guest molecule.     

Binding of hydrogen bonding solutes at liquid–vapour interfaces of molecular fluids

We have calculated the potential of mean force (PMF) for the transfer of a solute molecule across a liquid–vapour interface for four different systems: (a) one methanol molecule in water, (b) one water molecule in methanol, (c) one acetonitrile molecule in water and (d) one water molecule in acetonitrile by means of constrained molecular dynamics simulations. A minimum of the PMF is found near the Gibbs dividing surface for methanol and acetonitrile solutes although the degree of surface activity is found to be somewhat different due, in part, to varying hydrogen bonding nature of these two solutes.     

Rydberg atom mediated polar molecule interactions: a tool for molecular-state conditional quantum gates and individual addressability

We study the possibility to use interaction between a polar molecule in the ground electronic and vibrational state and a Rydberg atom to construct two-qubit gates between molecular qubits and to coherently control molecular states. A polar molecule within the electron orbit in a Rydberg atom can either shift the Rydberg state, or form a Rydberg molecule. Both the atomic shift and the Rydberg molecule states depend on the initial internal state of the polar molecule, resulting in molecular state dependent van der Waals or dipole-dipole interaction between Rydberg atoms. Rydberg atoms mediated interaction between polar molecules can be enhanced up to 10(3) times. We describe how the coupling between a polar molecule and a Rydberg atom can be applied to coherently control molecular states, and specifically, to individually address molecules in an optical lattice, and to non-destructively readout molecular qubits.     

Environmental‐Confinement‐Induced Stability Enhancement of Chiral Molecules

We computationally study the transition process of a chiral difluorobenzo[c]phenanthrene (DFBcPh) molecule within non‐polar fullerene C₂₆₀ to explore the confinement effect. We find blue‐shifts in the infrared and Raman spectra of the molecule inside the fullerene relative to those of isolated systems. Six types of spectrum features of the molecule appear in the 0–60 cm^?1 band. Interestingly, the energy barrier of the chiral transformation of the molecule is elevated by 15.88 kcal mol^?1 upon the confinement by the fullerene, indicating improvement in the stability of the enantiomers. The protection by C₂₆₀ lowers the highest occupied molecular orbital energy level and lifts the lowest unoccupied molecular orbital energy level of the chiral molecule such that the chiral molecule is further chemically stabilized. We concluded that the confinement environment has an impact at the nanoscale on the enantiomer transformation process of the chiral molecule.     

液态水几何构型的分子动力学模拟

利用ＭＣＹＬ势对液态水进行分子动力学模拟，以探求近程和远程相互作用及液体的有序结构对水分子几何构型的影响，并确定对液态中水分子几何构型起作用的主要范围。模拟给出的液态水中原子对径向分布函数和水分子键长键角的变化与实验值能较好地符合。研究结果表明，液态水分子几何构型除与氢键的形成有关外，还与液体的近程有序结构有很大关系。键长的变化对这种近程有序结构虽不敏感，但键角的变化则对此非常灵敏。液态中第二水合     

Generation and orientation of organoxenon molecule H-Xe-CCH in the gas phase

We report on the first observation of the organoxenon HXeCCH molecule in the gas phase. This molecule has been prepared in a molecular beam experiment by 193 nm photolysis of an acetylene molecule on Xe(n) clusters (n approximately 390). Subsequently the molecule has been oriented via the pseudo-first-order Stark effect in a strong electric field of the polarized laser light combined with the weak electrostatic field in the extraction region of a time-of-flight spectrometer. The experimental evidence for the oriented molecule has been provided by measurements of its photodissociation. For comparison, photolysis of C(2)H(2) on Ar(n) clusters (n approximately 280) has been measured. Here the analogous rare gas molecule HArCCH could not be generated. The interpretation of our experimental findings has been supported by ab initio calculations. In addition, the experiment together with the calculations reveals information on the photochemistry of the HXeCCH molecule. The 193 nm radiation excites the molecule predominantly into the 2 (1)Sigma(+) state, which cannot dissociate the Xe-H bond directly, but the system evolves along the Xe-C coordinate to a conical intersection of a slightly nonlinear configuration with the dissociative 1 (1)Pi state, which then dissociates the Xe-H bond.     

Ni2 分子的自旋极化效应

The density functional（B3P86）method has been used to optimize the structure of Ni2 molecule. Results show that the ground state for Ni2 molecule is 5 multiple state,not 1 multiple state and 3 multiple state the literatures concluded. That shows the spin polarization effect of Ni2 molecule of transition metal elements for the first time. They take 1 multiple state and 3 multiple state as the ground state of the Ni2 molecule because the minimal energy value of 1 multiple state,3 multiple state and 5 multiple state of Ni2 molecule are very close to each other. Meanwhile,we have not found out any spin pollution and the ground state wave function doesn't mingle with wave function with higher energy state. The result shows that the ground state for Ni2 molecule is 5 multiple state,which shows the spin polarization effect of Ni2 molecule of transition metal elements. That is,there exist 4 parallel spin electrons,at this time;the number of the non-conjugated electron is the most. These electrons occupy different spacious tracks so that the energy of Ni2 molecule reduces to the minimum. It shows that the effect of parallel spin of Ni2 molecule is larger than the effect of the conjugated molecule. It is obviously related to the effect of electron d delocalization. The Murrell-Sorbie potential function with the parameters for ground state for Ni2 molecule are also derived. Dissociation energy of the ground state Ni2 molecule is 1.835 eV,the equilibrium bond length is 0.2243 nm,and the vibration frequency is 262. 35 cm-1 . The force constants f2,f3 and f4 are 1.1901 aJ / nm2,-5.8723 aJ/nm3,21.2505 aJ/nm4 respectively.     

Remarks on the concept of an atom in a molecule and on charge transfer between atoms on molecule formation

Density functional theory provides a natural and rigorous definition of an atom in a molecule in its ground state: The molecular electron density is the sum of atomic densities, the atoms have the same chemical potential as does the molecule, and the atoms are minimally promoted from their ground states. These atoms in general are not spherical, and in general they bear nonintegral charges. Charge transfer on molecule formation is thereby uniquely defined. Calculations by Palke and by Guse are reviewed, in which the hydrogen atom is identified in the hydrogen molecule.     

非极性烷烃溶剂在聚乙烯膜中无限稀释扩散系数的测定

气相色谱法研究小分子溶剂与聚合物材料之间的相互作用是一种快速、准确、方便的方法,该方法可以用来研究多种小分子溶剂在聚合物中的溶解和扩散行为.通过气相色谱法测定了3种小分子烷烃溶剂(正庚烷、正壬烷和正癸烷)在固定液聚乙烯中的保留时间和半峰宽,用vanDeemter模型进行数据处理,得到3种小分子在聚乙烯膜中的无限稀释扩散系数.