超快多维红外光谱学:分子结构的时空分辨

利用时间分辨的超快二维红外(2DIR)光谱、稳态一维红外光谱等手段,本文探讨了从溶液中的小分子体系到生物大分子体系的超快振动特性及所反映的分子结构动力学过程。研究了五羰基溴化锰在四氯化碳中的时间分辨2DIR光谱,发现了分子对称性增强的13 CO配体的红外吸收信号,并利用2DIR对角峰和非对角峰表征了其与12 CO配体振动态的相互作用和分子内能量传递过程;实现了钌羰基配合物在光敏黄色蛋白突变体M100A上的定点标记,并研究了该外源标记物的羰基配体的结构动力学,发现了探针分子的振动光谱指纹对其所处的空间位置的敏感性,还发现该探针分子的振动扩散过程对水相中的蛋白质结构涨落具有灵敏性。

二羰基茂铁二聚体[CpFe(CO)2]2的中红外泵浦探测光谱

利用一维稳态红外光谱和5-μm泵浦探测红外光谱手段,结合量子化学计算,以非桥连三价羰基为探针,研究了二羰基茂铁二聚体[CpFe（CO）2]2在二氯甲烷中的结构和振动动力学.结果表明,[CpFe（CO）2]2两个主要结构（顺式cis和反式trans摩尔比为1.7）的振动态寿命和转动动力学都有一定不同.两种结构的两个羰基振动激发态的指数衰减过程都有一个〈1ps的快组分和一个-20ps的慢组分.我们认为前者与宽带激发所产生的振动相干态的快速失相过程有关,而后者属于典型的C≡O伸缩振动态寿命.此外,cis结构与溶剂的较强作用使得其转动衰减较慢.结果表明,非桥连羰基的红外吸收频率和振转动力学对分子结构和溶剂环境都非常敏感.

Local structure of calcium silicate melts from classical molecular dynamics simulation and a newly constructed thermodynamic model

The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.

Molecular dynamics simulation of relationship between local structure and dynamics during glass transition of Mg_7Zn_3 alloy

The rapid solidification process of Mg7Zn3 alloy was simulated by the molecular dynamics method. The relationship between the local structure and the dynamics during the liquid-glass transition was deeply investigated. It was found that the Mg-centered FK polyhedron and the Zn-centered icosahedron play a critical role in the formation of Mg7Zn3 metallic glass. The self-diffusion coefficients of Mg and Zn atoms deviate from the Arrhenius law near the melting temperature and then satisfy the power law. According to the time correlation functions of mean-square displacement, incoherent intermediate scattering function and non-Gaussian parameter, it was found that the β-relaxation in Mg7Zn3 supercooled liquid becomes more and more evident with decreasing temperature, and the α-relaxation time rapidly increases in the VFT law. Moreover, the smaller Zn atom has a faster relaxation behavior than the Mg atom. Some local atomic structures with short-range order have lower mobility, and they play a critical role in the appearance of cage effect in theβ-relaxation regime. The dynamics deviates from the Arrhenius law just at the temperature as the number of local atomic structures begins to rapidly increase. The dynamic glass transition temperature （Tc） is close to the glass transition point in structure （TgStr）.

Simulation study on non-linear effects of initial melt temperatures on microstructures during solidification process of liquid Mg_7Zn_3 alloy

The non-linear effects of different initial melt temperatures on the microstructure evolution during the solidification process of liquid Mg7Zn3 alloys were investigated by molecular dynamics simulation, The microstructure transformation mechanisms were analyzed by several methods. The system was found to be solidified into amorphous structures from different initial melt temperatures at the same cooling rate of 1×10^12 K/s, and the 1551 bond-type and the icosahedron basic cluster （12 0 12 0 ） played a key role in the microstructure transition. Different initial melt temperatures had significant effects on the final microstructures. These effects only can be clearly observed below the glass transition temperature Tg; and these effects are non-linearly related to the initial melt temperatures, and fluctuated in a certain range. However, the changes of the average atomic energy of the systems are still linearly related with the initial melt temperatures, namely, the higher the initial melt temperature is, the more stable the amorphous structure is and the stronger the glass forming ability will be.

Molecular Dynamics Study on Microstructure of Potassium Dihydrogen Phosphates Solution

Molecular dynamics simulations were carried out to study the internal energy and microstructure of potassium dihydrogen phosphates （KDP） solution at different temperatures. The water molecule was treated as a simple-point-charge model, while a seven-site model for the dihydrogen phosphate ion was adopted. The internal energy functions and the radial distribution functions of the solution were studied in detail. An unusually large local particle number density fluctuation was observed in the system at saturation temperature. It has been found that the specific heat of oversaturated solution is higher than that of unsaturated solution, which indicates the solution experiences a crystallization process below saturation temperature. The radial distribution function between the oxygen atom of water and the hydrogen atom of the dihydrogen phosphate ion shows a very strong hydrogen bond structure. There are strong interactions between potassium cation and oxygen atom of dihydrogen phosphate ion in KDP solution, and much more ion pairs were formed in saturated solution.

Atomistic simulation of defected magnesium hydroxide as flame retardants

The mechanical properties and the point defect energy of magnesium hydroxide（Mg（OH）2） were studied using the molecular dynamics. Moreover, the microelectronic structure of Mg（OH）2 with point defects in the bulk and on its surface were investigated using the first principles. The simulation results indicate that Mg（OH）2 was easily modified by other cations because of its strong, favorable interstitial and substitution defects via point defect energy calculation. Mg（OH）2 can provide high-efficiency flame retardancy because of the strong OH（OH Schottky defect） or H bond（H Frenkel defect and Schottky defect）. The potential model of Mg（OH）2 was established, and molecular dynamics simulation was used to investigate the relations between the crystal structure and the mechanical properties. Mg（OH）2 with special morphology such as nano-sheets was a prior consideration to maintain the composite mechanical properties. The detailed electronic structures of Mg（OH）2 with defects were determined. This work may provide theoretical guidance for choosing dopant element and reveal the element doping mechanism of Mg（OH）2.

Melting Behaviour of Shell-symmetric Aluminum Nanoparticles： Molecular Dynamics Simulation

Molecular dynamics simulations with embedded atom method potential were carried out for A1 nanoparticles of 561 atoms in three structures： icosahedron, decahedron, and truncated octahedron. The total potential energy and specific heat capacity were calculated to estimate the melting temperatures. The melting point is 540＋10 K for the icosahedral structure, 500±10 K for the decahedral structure, and 520±10 K for the truncated octahedral structure. With the results of mean square displacement, the bond order parameters and radius of gyration are consistent with the variation of total potential energy and specific heat capacity. The relaxation time and stretching parameters in the Kohlraush-William-Watts relaxation law were obtained by fitting the mean square displacement. The results show that the relationship between the relaxation time and the temperatures is in agreement with standard Arrhenius relation in the high temperature range.

Molecular Dynamics Simulations of Silica Nanotube： Structural and Vibrational Properties Under Different Temperatures

Four-, six-, and eight-membered ring silica nanotubes at temperatures from 300 K to 1600 K are relaxed by classical molecular dynamics simulations with three potential models. The simulation results indicate that the stability of the end rings of the three silica nanotubes gradually decreases with increase in temperature. The validity of the vibrational features of silica nanotubes is shown by the vibrational density of states. Infrared spectra on the silica nanotubes under different temperatures are investigated. A detailed assignment of each spectral peak to the corresponding vibrational mode of the three nanotubes has been addressed. The results are in good agreement with the other theoretical and experimental

Theoretical Study of Hydration Effects on the Selectivity of 18-Crown-6 Between K~＋ and Na~＋

A combination of molecular dynamics （MD） and density functional theory （DFT） calculations were used to study the hydration structures of K＋ and Na＋ ions under the confinement of 18-crown-6 in order to identify the role of water in the selectivity of 18-crown-6 towards K＋.The radial distribution functions,coordination num-bers,orientation structures and interaction energies were analyzed to investigate the hydration of K＋ and Na＋ in 18-crown-6/cation complexes.All calculations of K＋ and Na＋ in bulk water were also conducted for comparison.The simulation results show that the orientation distributions of the water molecules in the first coordination shell of K＋ are more sensitive to the confinement of 18-crown-6 than those of Na＋.It is more favorable to confine a K＋ in 18-crown-6 than a Na＋ in terms of interaction energy.Good agreement is obtained between MD results and DFT results.

Local structure changes of Cu55 cluster during heating

The structural relaxation of a cluster containing 55 atoms at elevated temperatures is simulated by molecular dynamics. The interatomic interactions are given by using the embedded atom method （EAM） potential. By decomposing the peaks of the radial distribution functions （RDFs） according to the pair analysis technique, the local structural patterns are identified for this cluster. During increasing temperature, structural changes of different shells determined by atom density profiles result in an abrupt increase in internal energy. The simulations show how local structural changes can strongly cause internal energy to change accordingly.

Orientation and Motion of Water Molecules at Air/Water Interface

Here we report a quantitative study of the orientational structure and motion of water molecule at the air/water interface. Analysis of Sum Frequency Generation （SFG） vibrational peak of the free O-H stretching band at 3700 cm^-1 in four experimental configurations showed that orientational motion of water molecule at air/water interface is libratory within a limited angular range. The free OH bond of the interracial water molecule is tilted around 33°from the interface normal and the orientational distribution or motion width is less than 15°. This picture is significantly different from the previous conclusion that the interracial water molecule orientation varies over a broad range within the ultrafast vibrational relaxation time, the only direct experimental study concluded for ultrafast and broad orient, ational motion of a liquid interface by Wei et al. （Phys. Rev. Lett. 86, 4799, （2001）） using single SFG experimental configuration.

Molecular Dynamics Simulations of Liquid Phosphorus at High Temperature and Pressure

By performing ab initio molecular dynamics simulations, we have investigated the microstructure, dynamical and electronic properties of liquid phosphorus （P） under high temperature and pressure. In our simulations, the calculated coordination number （CN） changes discontinuously with density, and seems to increase rapidly after liquid P is compressed to 2.5 g/cm3. Under compression, liquid P shows the first-order liquid-liquid phase transition from the molecular liquid composed of the tetrahedral P4 molecules to complex polymeric form with three-dimensional network structure, accompanied by the nonmetal to metal transition of the electronic structure. The order parameters Q6 and Q4 are sensitive to the microstructural change of liquid P. By calculating diffusion coefficients, we show the dynamical anomaly of liquid P by compression. At lower temperatures, a maximum exists at the diffusion coefficients as a function of density; at higher temperatures, the anomalous behavior is weakened. The excess entropy shows the same phenomena as the diffusion coefficients. By analysis of the angle distribution functions and angular limited triplet correlation functions, we can clearly find that the Peierls distortion in polymeric form of liquid P is reduced by further compression.

Density functional investigation on structural and electronic properties of small bimetallic Pb_(n)Ag_(n)(n=2–12)clusters

Structural and electronic properties of PbnAgn(n=2–12)clusters were investigated by density functional theory with generalized gradient approximation at BLYP level in DMol3 program package.The optimized bimetallic PbnAgn(n=2–12)clusters were viewed as the initial structures,then,those were calculated by ab initio molecular dynamics(AIMD)to search possible global minimum energy structures of PbnAgn clusters,finally,the ground state structures of PbnAgn(n=2–12)clusters were achieved.According to the structural evolution of lowest energy structures,Ag atoms prefer gather in the central sites while Pb atoms prefer external positions in PbnAgn(n=2–12)clusters,which is in excellent agreement with experimental results from literature and the application in metallurgy.The average binding energies,HOMO-LUMO gaps,vertical ionization potentials,vertical electron affinities,chemical hardnessη,HOMO orbits,LUMO orbits and density of states of PbnAgn(n=2–12)clusters were calculated.The results indicate that the values of HOMO-LUMO gaps,vertical ionization potentials,vertical electron affinities and chemical hardnessηshow obvious odd-even oscillations when n≤5,PbnAgn(n=2–12)clusters become less chemically stable and show insulator-to-metal transition with the variation of cluster size n,PbnAgn(n≥9)cluster are good candidates to study the properties of PbAg alloys.Those can be well explained by the density of states(DOS)distributions of Pb atoms and Ag atoms between–0.5 Ha and 0.25 Ha in PbnAgn(n=2–12)clusters.

Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase

The complex model of Thermus thermophilus xylose isomerase （TtXI） with D-xylose was constructed, and molecular dynamics （MD） simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration （Rg）, subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups： one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.

Relationship of glass forming ability and local structural properties of liquid Cu-Zr alloys

Molecular dynamics(MD) simulations were performed to investigate the glass forming ability(GFA) and microscopic structural properties of liquid Cu-Zr alloys.Based on the analysis of composition dependences of the reduced glass transition temperatures and the excess volume,we found that the Cu-Zr glasses have the largest GFA at Cu65Zr35 composition.To get more detailed information of local structure,we calculated the pair correlation functions,partial pair correlation functions,the excess entropy,chemical order parameter,coordination number,and Voronoi index of Cu-Zr liquids.We found that there exists an obvious and close relationship among the GFA,the excess entropy calculated using the total pair correlation functions,chemical order parameters,and some Cu centered cluster with Voronoi index <0,2,8,1> and Zr centered cluster with Voronoi index <0,3,6,4>,which all have nonlinear dependences on Cu/Zr concentration and have extreme values at liquid Cu65Zr35 composition.

Correlation between mixing enthalpy and structural order in liquid Mg−Si system

The mixing enthalpies and structural order in liquid Mg−Si system were investigated via ab-initio molecular dynamics at 1773 K.By calculating the transferred charges and electron density differences,the dominance of Si−Si interactions in the chemical environments around Si was demonstrated,which determined that the mixing enthalpy reached the minimum on Mg-rich side.In terms of Honeycutt and Anderson(HA)bond pairs based on the partial pair correlation functions,the attraction between Si−Si pairs and Mg atoms was revealed,and the evolution of structural order with Si content was characterized as a process of constituting frame structures by Si−Si pairs that dispersed Mg atoms.Focusing on tetrahedral order of local Si-configurations,a correlation between the mixing enthalpy and structural order was uncovered ultimately,which provided a new perspective combining the energetics with geometry to understand the liquid Mg−Si binary system.

Ultrafast Electron Diffraction with Spatiotemporal Resolution of Atomic Motion

Ultrafast electron diffraction （UED） is a rapidly advancing technique capable of recording the atomic-detail structural dynamics in real time. We report the establishment of the first UED system in China. Employing this UED apparatus, both the coherent and the concurrent thermal lattice motions in an aluminium thin-film, trigged by ultrafast laser heating, have been observed. These results demonstrate its ability to directly measure a sub-milli-angstrom lattice spacing change on a sub-picosecond time scale.

Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse-Grained Model

The secondary structure of different Iβ cellulose was analyzed by a molecular dynamics sim- ulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N of 4, 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N of 8, 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.

利用中子散射探索生命世界中的物理奥秘

中子散射是利用入射中子与原子核发生碰撞以后中子动量与能量的改变来研究微观世界的一种技术。由于中子对氢原子的散射截面远大于其他元素的独特属性,使得中子散射在研究包含大量氢元素的生物大分子的结构以及动力学特性方面都有卓越的应用。文章对中子散射在生物方面的应用进行了探讨,重点介绍了中子衍射、结合衬度变换技术的小角中子散射、准弹性/非弹性中子散射和中子自旋回波技术,以及它们在研究生物大分子结构、动力学及其功能方面的应用。最后对中子散射未来在生命科学中探索新的物理现象进行了探讨和展望。