钙离子调控微丝切割蛋白中A6亚基解折叠的单分子力谱研究

在生命活动中,金属离子扮演了非常重要的角色.微丝切割蛋白(adseverin)需要钙离子的活化才能行使其切割肌动蛋白微丝的功能.本文通过基于原子力显微镜的单分子力谱研究了微丝切割蛋白C端末的A6亚基在结合钙离子前后的力学解折叠机理.实验结果显示:在未结合钙离子时,A6的解折叠表现为两态过程;在结合钙离子后A6力学稳定性显著提高;同时,钙离子的结合使得A6解折叠过程中出现稳定的中间态.通过对中间态的链长的分析,我们推测了中间态对应着A6的N端部分解折叠.而这一部分的解折叠可以使得掩藏在该结构后的A5亚基中肌动蛋白微丝结合位点暴露,从而促使微丝切割蛋白执行功能.我们的实验结果为理解微丝切割蛋白的工作原理提供了新的实验证据.     

压力对硫醇分子膜电输运性质的影响

利用密度泛函理论和弹性散射格林函数方法,对硫醇分子膜的电学特性进行了理论模拟,计算结果表明,分子结的导电能力随着压力增加而增加,对单分子构成的分子结来说,电流的增加主要是由于电极距离的变化导致单个分子与电极的耦合增强,对于由多个分子构成的分子膜来说,由于外加压力的变化,导致分子结的链内隧穿和链间隧穿几率增大,从而导致导...     

The analytical potential energy function of flue gas SO₂（X¹A₁）

The equilibrium structure of flue gas SO 2 is optimized using the density functional theory (DFT)/ B3P86 method and CC-PV5Z basis. The result shows that it has a bent (C2V ,X1A1) ground state structure with an angle of 119.1184 . The vibronic frequencies and the force constants are also calculated. Based on the principles of atomic and molecular reaction statics (AMRS), the possible electronic states and reasonable dissociation limits for the ground state of SO2 molecule are determined. The potential functions of SO and O2 are fitted by the modified Murrell–Sorbie+c6 (M-S+c6) potential function and the fitted parameters, the force constants and the spectroscopic constants are obtained, which are all close to the experimental values. The analytic potential energy function of the SO2 (X1A1) molecule is derived using the many-body expansion theory. The contour lines are constructed, which show the static properties of SO2 (X1A1), such as the equilibrium structure, the lowest energies, the most possible reaction channel, etc.     

机械剥离折叠石墨烯粘附与纳米摩擦性质

本文用原子力显微镜研究了空气和氮气两种不同气氛环境下的机械剥离石墨烯粘附力,发现氮气环境下的粘附力更小,且石墨烯边缘的粘附力比内部区域大.在氮气环境下探究了折叠石墨烯粘附力与层数的关系及其摩擦性能,结果表明粘附力与折叠石墨烯层数无明显关系,折叠石墨烯各区域的摩擦性能都远超二氧化硅基底,且单层、单层上折叠、双层以及双层上折叠区域的摩擦系数依次降低,分别为0.049,0.031,0.023和0.021,摩擦力也依次降低,折叠处由于层与层之间的结合力弱于相同层数的石墨烯,摩擦性能有所降低,但未发现粘附力与摩擦力之间的明显关系.在采用尖针和球针测量粘附力时,测量历史不会对后续粘附力产生明显影响.对空气环境下出现的新鲜折叠石墨烯的研究表明新鲜折叠石墨烯的折叠区域摩擦力较未折叠区域显著增大.     

基于片层光照明的新型单分子横向磁镊

磁镊是一种高精度的单分子技术,它用磁场对连有生物大分子的超顺磁球产生磁力,通过追踪磁球的位置来测量生物大分子的长度信息.磁镊包括横向磁镊和纵向磁镊.纵向磁镊空间精度高,但昂贵;横向磁镊简单便宜,但由于受其成像原理的限制,一般情况下只能连接较长的DNA等生物大分子,且其空间精度较差,进而限制了其应用范围.为了解决这个问题,本文改进了横向磁镊,用片层光照明的方法使光线主要被磁球散射,从而能够直接观察到吸附在样品槽侧壁上的磁球,这使得测量短连接的底物成为可能.对于实际应用的检测,首先测试了包含270 bp发卡结构的0.5μm双链DNA,用其中发卡结构的"折叠-去折叠"跳变过程证明了改进后的横向磁镊的确可以追踪短DNA等生物大分子.然后,进一步用16μm的λ-DNA检验了实验系统.最后,将新型横向磁镊与普通横向磁镊及纵向磁镊在小力和大力条件下拉伸不同长度DNA的噪声进行了比较,发现改进后的横向磁镊在空间精度上明显优于普通横向磁镊,与纵向磁镊相比也无明显差异.以上结果证明了改进后的横向磁镊的精度优势,并扩展了横向磁镊的应用范围.     

The molecular structure and analytical potential energy function of HCO （X^2A＇）

In this paper the equilibrium structure of HCO has been optimized by using density functional theory （DFT）/ B3P86 method and CC-PVTZ basis. It has a bent （Cs, X^2A＇） ground state structure with an angle of 124.4095 °. The vibronic frequencies and force constants have also been calculated. Based on the principles of atomic and molecular reaction statics, the possible electronic states and reasonable dissociation limits for the ground state of HCO molecule have been determined. The analytic potential energy function of HCO （X^2A＇） molecule has been derived by using the many-body expansion theory. The contour lines are constructed, which show the static properties of HCO （X^2A＇）, such as the equilibrium structure, the lowest energies, etc. The potential energy surface of HCO （X^2A＇） is reasonable and very satisfactory.     

BeC，BeC2分子的结构与势能函数

应用密度泛函B3P86/aug-cc-pvtz方法对BeC(X )进行了理论计算,得到BeC分子基态的平衡核间距为0.1666 nm,离解能为2.3185eV,与其它理论结果符合得非常好,并进一步计算了谐振频率为917.9114 cm-1,得到该分子的Murrell-Sorbie势能函数。用QCISD/6-311++G（3df,3pd）方法优化出BeC2(X1A1)分子的稳定构型为C2V,其平衡核间距 =0.1615 nm、 ,并计算了离解能、力常数及谐振频率。在推导BeC2的离解极限基础上,应用多体展式理论方法,推导出基态BeC2分子的解析势能函数,该势能面准确呈现出BeC2`(X1A1)分子基态的结构特征和能量变化。     

BeC，BeC2分子的结构与势能函数

应用密度泛函B3P86/aug-cc-pvtz方法对BeC(X )进行了理论计算,得到BeC分子基态的平衡核间距为0.1666 nm,离解能为2.3185eV,与其它理论结果符合得非常好,并进一步计算了谐振频率为917.9114 cm-1,得到该分子的Murrell-Sorbie势能函数。用QCISD/6-311++G（3df,3pd）方法优化出BeC2(X1A1)分子的稳定构型为C2V,其平衡核间距 =0.1615 nm、 ,并计算了离解能、力常数及谐振频率。在推导BeC2的离解极限基础上,应用多体展式理论方法,推导出基态BeC2分子的解析势能函数,该势能面准确呈现出BeC2`(X1A1)分子基态的结构特征和能量变化。     

Carbon nanotubes as substrates for molecular spiropyran-based switches

We present a joint theory-experiment study investigating the excitonic absorption of spiropyran-functionalized carbon nanotubes. The functionalization is promising for engineering switches on a molecular level, since spiropyrans can be reversibly switched between two different conformations, inducing a distinguishable and measurable change of optical transition energies in the substrate nanotube. Here, we address the question of whether an optical read-out of such a molecular switch is possible. Combining density matrix and density functional theory, we first calculate the excitonic absorption of pristine and functionalized nanotubes. Depending on the switching state of the attached molecule, we observe a red-shift of transition energies by about 15?meV due to the coupling of excitons with the molecular dipole moment. Then we perform experiments measuring the absorption spectrum of functionalized carbon nanotubes for both conformations of the spiropyran molecule. We find good qualitative agreement between the theoretically predicted and experimentally measured red-shift, confirming the possibility for an optical read-out of the nanotube-based molecular switch.     

Quantum theory of chiral interactions in cholesteric liquid crystals

The effective chiral interaction between molecules arising from long-range quantum interactions between fluctuating charge moments is analyzed in terms of a simple model of chiral molecules. This model is based on the approximations that (a) the dominant excited states of a molecule form a band whose width is small compared to the average energy of excitation above the ground state and (b) biaxial orientational correlation between adjacent molecules can be neglected. Previous treatments of quantum chiral interactions have been based on a multipole expansion of the effective interaction energy within second-order perturbation theory. We consider a system consisting of elongated molecules and, although we invoke the expansion in terms of coordinates transverse to the long axis of constituent molecules, we treat the longitudinal coordinate exactly. Such an approximation is plausible for molecules in real liquid crystals. The macroscopic cholesteric wave vector Q (Q=2 pi/P, where P is the pitch) is obtained via Q=h/K(2), where K2 is the Frank elastic constant for twist and h is the torque field which we calculate from the effective chiral interaction kappa(IJ)a(I)xa(J) x R(IJ), where the unit vector a(I) specifies the orientation of molecule I and R(IJ) is the displacement of molecule I relative to molecule J. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. When both molecules are excited, we regain the R(-8)(IJ) dependence of kappa(IJ) on intermolecular separation found previously by Van der Meer et al. [J. Chem. Phys. 65, 3935 (1976)]. The two-molecule, unlike the one-molecule term, can be interpreted in terms of a superposition of pairwise interactions between individual atoms (or local chiral centers) on the two molecules. Contributions to kappa(IJ) when one molecule is excited in the virtual state are of order R(-7)(IJ) for helical molecules which are assumed not to have a global dipole moment, but whose atoms possess a dipole moment. It is shown that for a helical molecule Q can have either the same or the opposite sign as the chiral pitch of an individual molecule, depending on the details of the anisotropy of the atomic polarizability. The one-molecule mechanism can become important when the local atomic dipoles become sizable, although biaxial correlations (ignored here) should then be taken into account. Our results suggest how the architecture of molecular dipole moments might be adjusted to significantly influence the macroscopic pitch.     

分子间相互作用对硫醇分子膜电输运性质的影响

利用密度泛函理论和弹性散射格林函数方法,对硫醇分子膜的电学特性进行模拟.计算结果表明,由于分子间的相互作用,导致分子膜的导电能力比单分子提高2~3个数量级.分子结的导电能力随着压力增加而增加,电极距离的变化使分子与电极以及分子间的耦合增强、分子结的链内隧穿和链间隧穿几率增大,导致电流增加.     

Stopping a vibrational wave packet with laser-induced dipole forces

Intense near-infrared laser pulses can generate laser-induced dipole forces that are strong enough to influence or control vibrational motion of a small molecule. Generally, the force acts to pull the molecule apart. Our numerical simulations show that, by applying the laser-induced dipole force at an appropriate time within one vibrational period, the wave packet motion of H+2 or D+2 can be accelerated or decelerated. Using the wave packet formed by the rapid ionization of H2 or D2, we also show that it is possible to move the vibrational population almost entirely to the v=0 state. Coherent cooling of the molecular vibrational motion can be achieved.     

Spin polarization effect for Cr2 molecule

Density functional theory （DFT） （B3P86） of Gaussian 03 has been used to optimize the structure of the Cr2 molecule, a transition metal element molecule. The result shows that the ground state for the Cr2 molecule is a 13- multiple state, indicating that there exists a spin polarization effect in the Cr2 molecule. Meanwhile, we have not found any spin pollution because the wave function of the ground state does not mingle with wave functions of higher-energy states. So the ground state for Cr2 molecule being a 13-multiple state is indicative of spin polarization effect of the Cr2 molecule among transition metal elements, that is, there are 12 parallel spin electrons in the Cr2 molecule. The number of non-conjugated electrons is greatest. These electrons occupy different spatial orbitals so that the energy of the Cr2 molecule is minimized. It can be concluded that the effect of parallel spin in the Cr2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell Sorbie potential functions with the parameters for the ground state and other states of the Cr2 molecule are derived. The dissociation energy De for the ground state of the Cr2 molecule is 0.1034eV, equilibrium bond length Re is 0.3396 nm, and vibration frequency we is 73.81cm^-1. Its force constants f2, f3 and f4 are 0.0835, -0.2831 and 0.3535 aJ. nm^-4 respectively. The other spectroscopic data for the ground state of the Cr2 molecule ωeχe, Be and αe are 1.2105, 0.0562 and 7.2938 x 10^-4cm^-1 respectively.     

Probing protein-protein interactions by dynamic force correlation spectroscopy

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P(1)P(2)). The joint distribution P(tau(1),tau(2)) of unbinding lifetimes tau(1) and tau(2), measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of tau(1) is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P(1)P(2). We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.     

Appropriate Gate Time for Single Molecular Photon Detection Based on Optimal Signal-to-Noise Ratio Analyses

Signal-to-noise ratio of fluorescence detection from a single molecule ＆ analysed by using time-gated techniques. It is found that the optimal signal-to-noise ratio can be obtained by choosing an appropriate gate time with a certain optical background. The dependences of molecular fluorescence lifetime and the optimal signal-to-noise ratio on the appropriate gate time are respectively discussed with two kinds of background sources~ chaotic state with uniform distribution and coherent state with exponential distribution in time domain. For chaotic state background we find that a certain range for appropriate gate time can be obtained with a definite fluorescence lifetime, larger fluorescence lifetime would lower the value of optimal signal-to-noise ratios. For coherent state background we find that there is also a narrow range of appropriate gate time when lifetime of single molecule is less than that of background photons.     

非线型三原子分子势能面的Lie代数方法

利用Lie代数方法得到三原子分子的代数Hamiltonian ,通过对光谱数据的拟合确定其展开系数 ,再用相干态得到代数Hamiltonian的经典极限 ,从而得到三原子分子的势能面 .以H2 O分子为例进行了计算 ,其理论值与实验结果一致. The algebraic Hamiltonian for a triatomic molecule can be obtained by using dynamical Lie algebra method (the expansion coefficients are obtained by fitting spectroscopic data). Triatomic molecular potential energy surface (PES) is obtained by using coherent state to take the classical limits of algebraic Hamiltonian. This PES is applied to H 2O molecule, and the deduced force constant is in good agreement with the experimental data.     

Reversible bond formation in a gold-atom-organic-molecule complex as a molecular switch

We report on the formation of a metal-molecule complex that can be used as a molecular switch. Using a cryogenic scanning tunneling microscope, a covalent bond was formed reversibly between a gold atom and a perylene-3,4,9,10-tetracarboxylic dianhydride molecule supported by a thin insulating film. The bonded and the nonbonded state of the complex were found to be associated with different charge states, and the switching between the two states was accompanied by a considerable change in the tunneling current. Atomic force microscopy molecular imaging was employed to determine precisely the atomic structure of the complex, and the experimental results were corroborated by density functional theory calculations.     

外场对分子纳米结电流-电压特性的影响

针对由金属电极/分子/金属电极组成的分子纳米结,应用扩展主方程的方法,考虑分子纳米结中影响其传输过程的外场、分子内的弛豫过程等因素研究了在外场作用下分子纳米结内的稳定电流和瞬间电流.由于分子内较强的电子-振动耦合,分子纳米结中的电流-电压曲线呈现台阶式非弹性特征.在不同的高斯型脉冲的激发作用下,分子纳米结中电流需要达到稳定的时间也不相同,脉冲宽度在1ps时瞬间电流现象明显,这时分子处于非平衡分布,分子两端的电流存在较大差异.随着脉冲宽度和外场偏压的增加,分子两端的电流趋于平衡.     

分子的位置取向对分子器件电输运特性的影响

以1,4-二硫酚(DTB)分子为研究对象，利用第一性原理计算方法和非平衡格林函数理论，研究了分子的位置取向对分子电子结构以及分子结电输运性质的影响.计算结果表明，分子位置取向的改变会影响分子的电子结构，从而影响分子体系的电输运特性，扩展分子的平衡态不是电子输运的最佳状态，适当调节分子的位置取向可以提高分子的电输运特性. 关键词： 位置取向 电子输运 分子电子学     

用二极管激光探测法研究分子的动力学过程

本文介绍用二极管激光探测法研究分子的光解、碰撞、化学反应及能量转移等动力学过程.以高速原子和分子的碰撞过程为例进行了介绍.二极管激光探测法的分辨率比传统的红外荧光法提高一万倍,速率提高十倍,且灵敏度也较高.即使在有许多分子和众多量子态存在的情况下,该方法也能抓住待测分子或待测态,得到清楚的结果.目前可在3～30μm的范围内适用.