温度对液态水结构的影响：中子及X射线散射研究

采用中子散射和X射线散射研究了液态水在298～373 K温度范围内的结构,通过偏径向分布函数(PDF)、配位数分布(CN)、角分布(ADF)及空间密度分布(SDF)等讨论了温度对液态水结构的影响。整体来看,液态水具有"不规则四面体"氢键网络的短程有序结构,该有序度可延续到第三水合层。液态水分子的第一水合层中,围绕中心水分子约有4.8个水分子,然而其中仅有约3.3个水分子与中心水分子通过氢键相键合,约1/3进入到第一水合层的水分子并未与中心水分子直接键合,也正是这些间隙水分子的存在加剧了液态水结构的复杂性。温度对液态水的有序度存在一定的影响,在298～373 K的有限温度变化范围内,温度对液态水中氢键的键长、键角分布及第一水合层SDF的影响不大。从298K升温到373K,O(W)-O(W)距离仅增加0.03?,氢键数目也仅有微小减少,温度对第二和第三水合层的影响则要显著很多。     

金属Ni熔化前后结构变化的分子动力学模拟

使用Tight-binding势函数, 对FCC-Ni升温熔化过程的结构变化进行了分子动力学模拟. 在定压条件下模拟得到的Ni的熔点在1850 K与1900 K之间. 计算得到了体系在各温度下的径向分布函数和配位数分布等静态结构信息以及动力学性质. 计算得出的液体Ni的扩散系数在1900 K时约为5.02×10−9 m2•s−1, 与实验数据相符. 对液态体系中FCC短程有序结构可能发生的畸变以及由此导致的H-A键型变化进行了分析, 结合配位体构型搜索和键对分析方法计算了各温度下不同短程有序结构的分布. 计算表明, Ni在熔化之后仍保留有部分晶态短程结构, 但发生了较大的畸变, 同时液态中有少量的缺陷二十面体结构存在. 而液体Ni中大多数的配位体的几何构型介于FCC与缺陷二十面体之间.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150～376K的温度范围内对液态水的微正则系综进行了研究.考察了液态水的结构及其性质.模拟采用了由从头算得出的柔性水-水相互作用势MCYL.对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化.对径向分布函数g_(OH),goo,g_(HH)及配位数的分析表明,在所考察的温度范围内,每个水分子与相邻分子形成的氢键数为2～3,水分子在参与的2个氢键中同时作为接受体.结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构.     

硝胺及其甲基衍生物的从头计算研究 I: 平衡几何构型的全优化

我们用移植的TEXAS梯度法从头计算程序, 选取STO-4-21G基组, 对硝胺、甲硝胺和二甲硝胺等分子的平衡几何构型进行了全优化计算。其C-N, N-H和C-H等键长的计算结果以4-21G基组的标准校正值校正之后, 所得理论预测值与实验数据良好相符, 对N-N,N-O键长以及键角、两面角等构型参数, 对照计算和实验结果进行了讨论。     

硝胺及其甲基衍生物的从头计算研究 I: 平衡几何构型的全优化

我们用移植的TEXAS梯度法从头计算程序, 选取STO-4-21G基组, 对硝胺、甲硝胺和二甲硝胺等分子的平衡几何构型进行了全优化计算。其C-N, N-H和C-H等键长的计算结果以4-21G基组的标准校正值校正之后, 所得理论预测值与实验数据良好相符, 对N-N,N-O键长以及键角、两面角等构型参数, 对照计算和实验结果进行了讨论。     

晶体结构分析中键长、键角标准偏差及其计算程序(GCSD)

在晶体结构分析中,测定了分子的键长和键角以后,还应当指明它们的标准偏差。这对于进一步确定分子的键长和键角的变异情况,分子空间结构的微细变化与其化学性质的关系,以及按量子化学理论计算所得的键长、键角值与真实结构符合的程度等方面都     

应用晶体结构数据进行化学反应途径研究 Ⅰ五配位钼化合物Mo(L)_5的动态立体化学

在国内首次采用结构相关法分析了28个晶体结构中所含44个Mo(L)_5片断。分子几何的定义见图1.五配位的化合物包括两个构型:三方双锥体(TBP)和四方单锥体(SQP)多面体中面间交角(二面角δ_(ij))的定义如图2.配位原子编号的优先次序为L_1和L_5间含有最大键角θ_(15),且d_5>d_1(d_i为键长增量,为晶体结构中实际测得的键长减去标准键长而得,标准键长的数值取自文献),L_2和L_4含有次大的键角θ_(24),另一个则标为L_3.     

水分子配位对叶绿素a氧化还原势与红外光谱的影响

以光系统I反应中心电子传递链上的辅助叶绿素a为目标,采用密度泛函理论中的B3LYP方法,结合三种基组,系统计算了该叶绿素及其两种配位分子模型在气相、模拟蛋白质环境和水中的氧化还原势和离解能;同时计算了这三种模型在气相中的几何结构、红外光谱及其13C、15N和2H的同位素标记谱.计算及分析结果表明:水分子配位引起镁离子偏离叶绿素a的卟啉环平面中央,导致以镁原子为中心的键角减小,Mg—N键长增长;而天冬酰胺对配位的水分子施加氢键影响后,使得Mg—N键进一步增长,镁离子与水分子中氧原子的配位键Mg—O键长减小,离解能增加,合成分子的氧化还原势减少;另外,分子的氧化还原势和配位键离解能随着相对介电常数的增加以及计算基组的增大而减小;三种分子模型的羰基(C襒O)和卟啉环上C襒C键的特征振动频率差值小于7cm-1,而同位素标记引起其峰位变化量的差值小于3cm-1.该计算为研究光合反应中心电子传递链上叶绿素a的作用与功能提供理论参考依据.     

相对论赝势的从头计算法研究铀酰离子电子结构

用相对论赝势的从头算法研究了铀酰离子的几何构型和电子结构.得到了与实验数据较一致的键长、键角和IR振动频率.铀氧间以U5f与O2p相互作用为主,U6d与O2p间的键合较小;同时,U6p、U7s、U6d和Usd杂化轨道与O2s间也有强的相互作用.不同自旋多重度时对铀酰离子总能量计算结果表明,UO22+的基态为1∑g+的可能性更大.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.     

Flexible simple point-charge water model with improved liquid-state properties

In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of the intramolecular degrees of freedom on liquid properties was systematically studied in this work as a function of many possible parameter sets. It was found that the diffusion constant is extremely sensitive to the equilibrium bond length and that this effect is mainly due to the strength of intermolecular hydrogen bonds. The static dielectric constant was found to be very sensitive to the equilibrium bond angle via the distribution of intermolecular angles in the liquid: A larger bond angle will increase the angle formed by two molecular dipoles, which is particularly significant for the first solvation shell. This result is in agreement with the work of Hochtl et al. [J. Chem. Phys. 109, 4927 (1998)]. A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle. Due to the large sensitivities, the parametrization only slightly perturbs the molecular geometry of the base SPC model. Extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC model.     

Correlation of hydrogen bond lengths and angles in liquid water based on Compton scattering

The temperature-dependent hydrogen-bond geometry in liquid water is studied by x-ray Compton scattering using synchrotron radiation combined with density functional theory analysis. Systematic changes, related to the weakening of hydrogen bonding, are observed in the shape of the Compton profile upon increasing the temperature. Using model calculations and published distribution functions of hydrogen-bond geometries obtained from a NMR study we find a significant correlation between the hydrogen-bond length and angle. This imposes a new constraint on the possible local structure distributions in liquid water. In particular, the angular distortions of the short hydrogen bonds are significantly restricted.     

The value of the π-bond order–bond length relationship in geometry prediction and chemical bonding interpretation

The π-bond order–bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π-bond order and overlap population results for carbon–carbon, carbon–nitrogen, and carbon–oxygen bonds obtained from ab initio STO -3G calculations using theoretically-optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order–length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp² – sp² and sp – sp hybridized C? C, C? N, and C? O bonds, and in evaluating the relative importance of hybridization, π-electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π-bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4-21G basis set are also presented.     

Structures of photo-produced transient species

An overview of recent advances in the experimental measurements, theoretical interpretations, and practical applications of bond length and bond angle changes that occur after a molecule absorbs one or more photons is presented. “Gentle” changes are those in which the chemical bonds remain intact, but the lengths and angles increase or decrease. The bond length and bond angle changes that occur when a molecule absorbs a photon are measured by using a combination of electronic (emission and absorption) spectroscopy, resonance Raman spectroscopy, and the time-dependent theory of spectroscopy. “Catastrophic” changes are those in which multiple bonds are broken, leading to extensive photofragmentation. Luminescence spectroscopy is used to identify the transient fragments of metal-containing compounds that are precursors for laser assisted chemical vapor deposition.     

An electron diffraction study of the molecular structure of hexamethyldisiloxane

An electron diffraction determination of the molecular geometry of hexamethyldisiloxane has removed much of the uncertainty concerning this structure. The length of the SiO bond and the SiOSi bond angle were determined to be 1.631 ± 0.003 Å and 148 ± 3°, respectively. The experimental data are consistent with a staggered conformation (C_2v symmetry) while a model with twist angles around the SiO bonds of about 30° cannot be excluded. The molecule is probably performing large amplitude intramolecular motion.     

羟烷基胺功能化离子液体吸收SO_2的量子化学计算(英文)

采用量子化学中的密度泛函理论(DFT)对羟烷基胺离子液体(HyAAILs)与二氧化硫(SO2)的相互作用进行了研究.通过几何结构优化,电荷分布和热力学参数计算等来确定离子液体中能够有效吸收SO2的官能团.HyAAILs与SO2反应形成平均距离为0.240nm的S—N键,导致电荷从ILs转移到SO2以及S—O键长和O—S—O键角的改变.气态和液态模型的计算结果表明,标准吉布斯函数变(△G苓)主要取决于阳离子的结构和分子质量.阳离子结构影响了吸收反应能垒,对于三种阳离子体系的反应活化能顺序为:Ea(secondary)Ea(tertiary)Ea(primary).理论计算结果得到了实验数据的验证,羟乙基伯胺离子液体吸收的SO2理论摩尔分数与文献中的实验数据非常接近.本研究提供了一种预测和验证功能离子液体性质的有效方法.     

Quasilinear molecule par excellence, SrCl2: structure from high-temperature gas-phase electron diffraction and quantum-chemical calculations--computed structures of SrCl2.argon complexes

The molecular geometry of strontium dichloride has been determined by high-temperature electron diffraction (ED) and computational techniques. The computation at the MP2 level of theory yields a shallow bending potential with a barrier of about 0.1 kcal mol(-1) at the linear configuration. The experimentally determined thermal average Sr--Cl bond length, r(g), is 2.625+/-0.010 A and the bond angle, angle-spherical(a), is 142.4+/-4.0 degrees . There is excellent agreement between the equilibrium bond lengths estimated from the experimental data, 2.607+/-0.013 A, and computed at different levels of theory and basis sets, 2.605+/-0.006 A. Based on anharmonic analyses of the symmetric and asymmetric stretching as well as the bending motions of the molecule, we estimated the thermal average structure from the computation for the temperature of the ED experiment. In order to emulate the effect of the matrix environment on the measured vibrational frequencies, a series of complexes with argon atoms, SrCl(2)Ar(n) (n=1-7), with different geometrical arrangements were calculated. The complexes with six or seven argon atoms approximate the interaction best and the computed frequencies of these molecules are closer to the experimental ones than those computed for the free SrCl(2) molecule.     

Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.