N-(1-萘基)-琥珀酰亚胺化合物晶体结构的理论预测

用Materials Studio软件对N-(1-萘基)-琥珀酰亚胺多晶粉末的X射线衍射数据进行衍射峰指标化、晶胞参数优化和空间群搜索等理论计算, 可以确定晶体结构所属的晶系和空间群, 并初步给出和多晶粉末衍射数据相近的晶胞参数; 在已确定空间群范围内, 以密度泛函理论计算得到的最低能量构象作为初始分子结构, 对N-(1-萘基)-琥珀酰亚胺多晶进行晶体结构理论预测, 给出一系列假定的晶胞参数, 从中可以找到和经上述计算给出的晶胞参数一致的晶体结构；对其进行晶胞参数优化后, 得到晶体结构具有和多晶粉末X射线衍射数据相近的衍射曲线, 并与已有的单晶数据相吻合.     

The crystal structure and low temperature magnetic susceptibility of square-planar bis(1,5-diazacyclooctane)nickel(II) perchlorate dihydrate

Summary We have carried out low temperature magnetic susceptibility measurements and a redetermination of the crystal and molecular structure of bis(1,5-diazacyclooctane)nickel(II) perchlorate dihydrate from three-dimensional intensity data collected on a CAD4 diffractometer. The structure was refined by full-matrix least-squares to the R value of 6.3% for 1501 observed reflections. The positions of the hydrogen atoms were obtained from the diffraction data. Contrary to our earlier conclusions drawn by inspection of molecular models of bis(diazacyclooctane) complexes, the axial sites in the actual crystal structure are open for ligation. The Ni-N bonds are, however, sterically protected by the coplanar N-H bonds, allowing maximum ligand-field stabilization for the squareplanar geometry around the nickel atom. The observed magnetic transition from a diamagnetic state at room temperature to a paramagnetic state at 78 K is explained on the basis of long-range exchange interactions along sterically unshieldedz axis. The crystal structure is compared with other similar structures.     

Ultraviolet stability of liquid crystals containing cyano and isothiocyanato terminal groups

The ultraviolet (UV) stabilities of liquid crystal compounds containing cyano (CN) and isothiocyanato (NCS) terminal groups are compared. UV exposure is found to degrade the clearing temperature, birefringence, dielectric constants and visco-elastic coefficient of the liquid crystal compounds. The measured data show that the NCS molecular structure exhibits a better UV stability than do the corresponding CN structures. Lewis resonance structures are used to explain this phenomenon.     

Ultraviolet stability of liquid crystals containing cyano and isothiocyanato terminal groups

The ultraviolet (UV) stabilities of liquid crystal compounds containing cyano (CN) and isothiocyanato (NCS) terminal groups are compared. UV exposure is found to degrade the clearing temperature, birefringence, dielectric constants and visco-elastic coefficient of the liquid crystal compounds. The measured data show that the NCS molecular structure exhibits a better UV stability than do the corresponding CN structures. Lewis resonance structures are used to explain this phenomenon.     

Urea: an ab initio and force field study of the gas and solid phases

We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range.     

Thermal behaviour of hydrated copper(II) complexes

Dehydration steps of aquacopper(II) complexes with homogeneous and heterogeneous coordination sphere are investigated from the view point of structural changes taking place under their heating to the decomposition temperature and during the dehydration. The role of loosening of intra-and intermolecular hydrogen bonds in the decomposition reaction for the structure changes of the remainder, the structural presumptions of the reactants for lower hydrates formation are discussed. Activation parameters of dehydration were found to be the lower, the smaller are the structure differences between the reactants and products. They do not reflect the bond length central atomvolatile ligand, much more the overall structure differences between the starting and resulting compounds. From all data on crystal and molecular structures of dehydrated compounds is the reaction pathway best indicated by anisotropic temperature parameters of donor atoms corrected for the thermal movement of the central atom: the higher these values in the bond direction are, the lower the values of activation energies of dehydration are.     

Application of molecular mechanics to refine and understand the crystal structure of polythiophene and its oligomers

A molecular mechanics computational procedure, previously used for the refinement and the analysis of several crystalline polymers, was applied to investigate the crystal structures of the tetramer (T4) and hexamer (T6) of thiophene, as well as the crystal structure of polythiophene (PT). Simultaneous minimization of intra- and intermolecular energies of the T4 and T6 structures, obtained by Rietveld analysis of powder X-ray diffraction profiles, leads to molecular conformations showing smaller deviations from the ring co-planarity than the original models. For both oligomers the calculations confirm that the molecular centre of inversion is not a crystallographic centre of symmetry, as also revealed by X-ray diffraction of the T6 single crystal. This surprising effect appears to arise from intermolecular interactions between the terminal residues, hence is not relevant with respect to the PT polymer structure. The small energy cost for constraining the molecules at the crystallographic centre of symmetry is in agreement with experimental findings that reveal the existence of polymorphs for both T4 and T6. The calculations on the T6 single crystal were used to upgrade the MM2-like force field, which was then used to determine the minimum-energy model of the monoclinic crystal structure of polythiophene.     

A crystallographic, EPR and theoretical study of the Jahn-Teller distortion in [CuTp2] (Tp- = tris[pyrazol-1-yl]hydridoborate)

Crystals of the title compound (1) contain two independent, centrosymmetric half-molecules per asymmetric unit. While both of these show Jahn-Teller elongated six-coordinate geometries, the lengths of the elongated Cu-N bonds in the two molecules differ by 0.117(2) A at 30 K. The structure of one of these molecules (molecule A) does not vary with temperature below 350 K. The other molecule (molecule B) shows Cu-N bond lengths that are temperature-dependent between 225 and 375 K, but do not vary further at lower temperature. This indicates a fluxional axis of Jahn-Teller elongation in this molecule at these higher temperatures. Consideration of the thermal parameters in these structures implies that the fluxionality in molecule B is frozen out near 150 K. This conclusion is supported by a Q-band powder EPR study. The d-d transition energies of molecules A and B have been calculated by several density function (DF) methods, including a time-dependent DF calculation. The crystallographic data have been reproduced using the vibronic coupling model of Burgi and Hitchman. This has shown that the different fluxionality regimes for molecules A and B are not a consequence of their different static molecular structures, but rather reflect their different local environments in the crystal.     

Theoretical studies of solid bicyclo-HMX: effects of hydrostatic pressure and temperature

On the basis of density functional theory (DFT) and molecular dynamics (MD), the structural, electronic, and mechanical properties of the energetic material bicyclo-HMX have been studied. The crystal structure optimized by the LDA/CA-PZ method compares well with the experimental data. Band structure and density of states calculations indicate that bicyclo-HMX is an insulator with the band gap of ca. 3.4 eV and the N-NO(2) bond is the reaction center. The pressure effect on the bulk structure and properties has been investigated in the range of 0-400 GPa. The crystal structure and electronic character change slightly as the pressure increases from 0 to 10 GPa; when the pressure is over 10 GPa, further increment of the pressure determines significant changes of the structures and large broadening of the electronic bands together with the band gap decreasing sharply. There is a larger compression along the c-axis than along the a- and b-axes. To investigate the influence of temperature on the bulk structure and properties, isothermal-isobaric MD simulations are performed on bicyclo-HMX in the temperature range of 5-400 K. It is found that the increase of temperature does not significantly change the crystal structure. The thermal expansion coefficients calculated for the model indicate anisotropic behavior with slightly larger expansion along the a- and c-axes than along the b-axis.     

Thermal response in crystalline Ibeta cellulose: a molecular dynamics study

The influence of temperature on structure and properties of the cellulose Ibeta crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles alpha and beta divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'...O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30 degrees . Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.     

Influence of the Temperature on the Crystal Structure of Poly(p‐phenylene sulfide): A Study by X‐Ray Measurements and Molecular Mechanics

The crystal structure of poly(p‐phenylene sulfide) (PPS) has been investigated by X‐ray analysis on fiber samples and by molecular mechanics calculations over a wide range of temperatures, from 0 K to 548 K, showing that all the structural parameters remain substantially constant. The thermal expansion coefficients of the a and b axes have been evaluated. Structural parameters experimentally obtained at the various temperatures have been used in calculations by molecular mechanics. The crystal structures calculated by various methods and using several potential functions are in very good agreement. New parameters are proposed for the nonbonded terms of the potential functions.     

壳聚糖超声可控降解及降解动力学研究

通过正交实验法考察了壳聚糖溶液浓度、反应温度、超声强度以及醋酸溶液浓度对超声降解反应的影响,确定了最佳反应条件,制备了一系列不同分子量的壳聚糖.研究了壳聚糖溶液浓度、反应温度以及壳聚糖原料分子参数与降解速率常数的关系.通过红外光谱、X-射线衍射和凝胶渗透色谱对降解产物进行了表征.结果表明,超声降解壳聚糖的最佳条件为10℃,壳聚糖溶液浓度2.5g/L.降解速率常数随壳聚糖溶液浓度和反应温度的降低而增大.高分子量和低脱乙酰度的壳聚糖原料有较高的降解速率和降解速率常数,壳聚糖原料的分子量对降解速率和降解速率常数的影响大于脱乙酰度对其的影响.超声波导致了壳聚糖分子量的降低和产物晶体结构的破坏,但没有改变产物的脱乙酰度和糖残基结构.     

Theoretical investigations of candidate crystal structures for β-carbonic acid

Using multiple computational tools, we examine five candidate crystal structures for β-carbonic acid, a molecular crystal of environmental and astrophysical significance. These crystals comprise of hydrogen bonded molecules in either sheetlike or chainlike topologies. Gas phase quantum calculations, empirical force field based crystal structure search, and periodic density functional theory based calculations and finite temperature simulations of these crystals have been carried out. The infrared spectrum calculated from density functional theory based molecular dynamics simulations compares well with experimental data. Results suggest crystals with one-dimensional hydrogen bonding topologies (chainlike) to be more stable than those with two-dimensional (sheetlike) hydrogen bonding networks. We predict that these structures can be distinguished on the basis of their far infrared spectra.     

Temperature Dependence of the Crystal Structure and EPR Spectrum of Bis(1,3,5-Trihydroxycyclohexane)copper(II) Tosylate. A Unified Interpretation Using a Model of Dynamic Vibronic Coupling

The crystal structure of bis(1,3,5-trihydroxycyclohexane)copper(II) tosylate is reported at temperatures of 293, 233, 188, 163, and 93 K, as are the structures of the Zn(II) and Ni(II) analogues at room temperature for comparison. The isomorphous compounds are triclinic, space group P&onemacr;, with one formula unit in the unit cell. The unit cell parameters of the Cu compound at 293 K are a = 6.456(5) ?, b = 9.505(3) ?, c = 12.544(3) ?, alpha = 76.57(2) degrees, beta = 87.48(4) degrees, gamma = 76.65(4) degrees. The centrosymmetric ZnO(6) and NiO(6) octahedra are tetragonally compressed with a slight orthorhombic distortion. The Cu(2+) polyhedra exhibit similar geometries, but with considerably larger deviations from a regular octahedron. Two of the three independent Cu-O bond lengths and two of the g-values change significantly as a function of temperature. A model of dynamic vibronic coupling is presented which explains both the EPR and structural data. Vibronic wave functions associated with a Jahn-Teller potential energy surface modified by an orthorhombic lattice "strain" are given. The temperature dependence of the structures is calculated from the nuclear parts and that of the g-values from the electronic parts of the wave functions. The temperature dependence of the structures and g-values is also interpreted using a simpler model involving an equilibrium between two forms of the complex which differ solely in their orientation in the crystal lattice, and the results of the two approaches are compared.     

Theoretical Simulations of Thermochromic and Aggregation-Induced Emission Behaviors of a Series of Red-Light Anthracene-o-carborane Derivatives

Quantum mechanical and molecular dynamics simulations have been carried out on a series of anthracene-o-carborane derivatives (ANT-H, ANT-Ph, ANT-Me and ANT-TMS) with rare red-light emission in the solid state. The simulation of the heating process of the crystals and further comparison of the molecular structures and excited-state properties before and after heating help us to disclose the thermochromic behavior, that is, the red-shift emission is caused by elongation of the C1−C2 bond in the carborane moiety after heating. Thus, we believe that the molecular structure in the crystal is severely affected by heating. Transformation of the molecular conformation appears in the ANT-H crystal with increasing temperature. More specifically, the anthracene moiety moves from nearly parallel to the C1−C2 bond to nearly perpendicular, causing the short-wavelength emission to disappear after heating. As for the aggregation-induced emission phenomenon, the structures and photophysical properties were investigated comparatively in both the isolated and crystal states; the results suggested that the energy dissipation in crystal surroundings was greatly reduced through hindering structure relaxation from the excited to the ground state. We expect that discussion of the thermochromic behavior will provide a new analysis perspective for the molecular design of o-carborane derivatives.     

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.     

钪、钇的电子结构和物理性质

依据金属单原子理论确定了密排六方结构α－Ｓｃ和α－Ｙ的电子结构分别为「Ａｒ」（３ｄｃ）＾１．３３１５（４ｓｃ）＾０．９０５０（４ｓｆ）＾０．７６３５和「Ｋｒ」（４ｄｃ）＾１．２９３０（５ｓｃ）＾０．９４７０（５ｓｆ）＾０．７６００,并计算了它们的势能曲线、晶格常数、结合能、弹性和热膨胀系数随温度的变化。对其体立方结构初态特征晶体和实态液体的电子结构进行了。提出了不同晶体结构Ｓｃ和Ｙ的结构构参数和性     

软胶体粒子形成束晶的动力学模拟

利用广义指数模型描述软胶体粒子, 结合分子动力学模拟研究软胶体粒子形成束晶的动力学过程. 通过等温压缩和等密度降温2个不同的过程, 研究了束晶形成过程中结构变化特征和动力学路径对结构的影响规律. 研究发现, 与蒙特卡洛模拟结果相比, 分子动力学模拟得到的结构随着密度的变化有明显的迟滞现象, 这是由于考虑了真实的动力学因素引起的差异. 此外, 在相同温度和压力下通过不同的动力学路径得到的相结构不完全相同, 这是由于动力学形成过程会对相结构产生很大的影响.     

Melting and homogeneous crystallization of a Lennard-Jones system

Melting and homogeneous crystallization in a Lennard-Jones system of 10,976 atoms in a model box with periodic boundary conditions were investigated by the molecular dynamics method in an NVE ensemble. Crystal melting occurs by arbitrary generation and growth of local defects transformed into regions of a disordered phase. These defects gradually span the entire space of the sample, absorbing the residual islands of crystal. Homogeneous crystallization of a liquid starts with generation of crystal nuclei which grow into defective crystals. The resulting crystal varies in structure between different realizations of the model. Face-centered cubic (fcc) structures prevail. A hexagonal close packing (hcp) structure is present on the boundaries of fcc regions and arises from disordering in alternation of atomic planes. Multiple twinning of the fcc structure is observed, and aggregates with fivefold symmetry have been found.