Four phases of amorphous water: Simulations versus experiment

Multiplicity of the liquid-liquid phase transitions in supercooled water, first obtained in computer simulations [Brovchenko et al., J. Chem. Phys. 118, 9473 (2003)], has got strong support from the recent experimental observation of the two phase transitions between amorphous ices [Loerting et al., Phys. Rev. Lett. 96, 025702 (2006)]. These experimental results allow assignment of the four amorphous water phases (I-IV) obtained in simulations to the three kinds of amorphous ices. Water phase I (rho approximately 0.90 gcm(3)) corresponds to the low-density amorphous ice, phase III (rho approximately 1.10 gcm(3)) to the high-density amorphous ice, and phase IV (rho approximately 1.20 gcm(3)) to the very-high-density amorphous ice. Phase II of model water with density rho approximately 1.00 gcm(3) corresponds to the normal-density water. Such assignment is confirmed by the comparison of the structural functions of the amorphous phases of model water and real water. In phases I and II the first and second coordination shells are clearly divided. Phase I consists mainly of the four coordinated tetrahedrally ordered water molecules. Phase II is enriched with molecules, which have tetrahedrally ordered four nearest neighbors and up six molecules in the first coordination shell. Majority of the molecules in phase III still have tetrahedrally ordered four nearest neighbors. Transition from phase III to phase IV is characterized by a noticeable drop of tetrahedral order, and phase IV consists mainly of molecules with highly isotropic angular distribution of the nearest neighbors. Relation between the structures of amorphous water phases, crystalline ices, and liquid water is discussed.     

Configurational probabilities for monomers, dimers and trimers in fluids

A new analytical approach is proposed to model aggregation of molecules with isotropic, nearest-neighbor, attractive interactions. By treating the clustering process as a chain reaction, equations with the exact high temperature limit are derived by evaluating the occupation probabilities of nearest neighbors based on the Ono-Kondo approach for a hexagonal lattice to calculate the configurational probabilities of i-mers (i = 1, 2, 3). Equilibrium constants for dimers and trimers are calculated based on the configurational probability data. The proposed model agrees well with Monte Carlo simulations at medium and high temperatures. At low temperatures, the model can be improved by considering the full set of site densities in the first shell of a central trimer. Approximate analytical solutions derived from exact calculations of the grand partition function for monomer adsorption on a 4 x N hexagonal lattice with cylindrical boundary conditions also are presented.     

Results of a new classification algorithm combining K nearest neighbors and recursive partitioning

We present results of a new computational learning algorithm combining favorable elements of two well-known techniques: K nearest neighbors and recursive partitioning. Like K nearest neighbors, the method provides an independent prediction for each test sample under consideration, while like recursive partitioning, it incorporates an automatic selection of important input variables for model construction. The new method is applied to the problem of correctly classifying a set of chemical data samples designated as being either active or inactive in a biological screen. Training is performed at varying levels of intrinsic model complexity, and classification performance is compared to that of both K nearest neighbor and recursive partitioning models trained using the identical protocol. We find that the cross-validated performance of the new method outperforms both of these standard techniques over a considerable range of user parameters. We discuss advantages and drawbacks of the new method, with particular emphasis on its parameter robustness, required training time, and performance with respect to chemical structural class.     

Path integral theory: An improved simulation for the forces in semiclassic systems

A method is proposed for calculating the forces in path integral theory and tested on semiclassic systems. It takes the range of the classic and quantum interactions into account and uses a second table within the neighbors table for the nearest neighbors. This method is found to be much more efficient than either the standard direct method or the traditional neighbors table, the efficiency increasing with the size of the system. The method can also be applied to clusters whose interaction centers are much farther apart than the distances between two consecutive members of the cluster. © 1993 John Wiley & Sons, Inc.     

Properties of the network of the hydrogen bonds of water

Networks of the hydrogen bonds and those consisting of lines connecting nearby molecules were constructed using configurations of water molecules obtained by the Monte-Carlo method. The concentrations of closed cycles of hydrogen bonds were established to be determined only by the probability of hydrogen bond formation. Characteristics of a model ideal water network were determined. Topological properties of the Polk model and those of the network of nearest neighbors substantially differ from the properties of the ideal network. The totality of the hydrogen bonds in pure water was proposed to be considered as a hierarchical system. Three topologically different structures of water associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 928–931, May, 1997.     

A universal description of a solid crystal and liquid using discrete distribution functions

The numerical implementation of a crystallization/melting theory that has two branches of isotherms for liquids and solids as in Landau’s theory within the general self-consistent theory of condensed states is discussed. Equations are based on discrete distribution functions (the lattice gas model). Molecular distributions are calculated to a quasi-chemical approximation reflecting the effects of direct correlations between interacting particles. the interaction between particles is described by the Lennard-Jones potential, while the vibrational motion of molecules is included using a modified quasi-dimer Mie model. The effect of the vibrations of atoms on lateral interactions between nearest and next nearest neighbors is considered, along with a scheme for considering the displacement of particles in a liquid that modify such lateral interactions. Examples of calculations describing a defective crystal and vapor-liquid system are given.     

Computer simulation investigation of the water-benzene interface in a broad range of thermodynamic States from ambient to supercritical conditions

The dependence of the properties of the water-benzene system on the thermodynamic conditions in a broad range of temperatures and pressures has been investigated by computer simulation methods. For this purpose, Monte Carlo simulations have been performed at 23 different thermodynamic states, ranging from ambient to supercritical conditions. The density profiles of the water and benzene molecules have been determined at each of the thermodynamic states investigated. Information on the dependence of the mutual solubility of the two components in each other as well as of the width of the interface on the temperature and pressure has been extracted from these profiles. The width of the interface has been found to increase with increasing temperature up to a certain point, where it diverges. The temperature of this divergence corresponds to the mixing of the two phases. The determination of the critical mixing temperature at various pressures allowed us to estimate the upper critical curve, separating the two-phase and one-phase liquid systems, of the phase diagram of the simulated water-benzene system. In analyzing the preferential orientation of the interfacial molecules relative to the interface, it has been found that the main orientational preference of the benzene molecules is to lie parallel with the plane of the interface, and the water molecules penetrated deepest into the benzene phase prefer to stay perpendicular to the interface, pointing by one of their O-H bonds almost straight toward the benzene phase, whereas the waters located at the aqueous side of the interface are preferentially aligned parallel with the interfacial plane. Although the strength of the observed orientational preferences decreases rapidly with increasing temperature, the preferred orientations themselves are found to be independent of the thermodynamic conditions. Remains of the orientational preferences of the molecules are found to be present up to temperatures as high as 650 K. The analysis of the relative orientation of the neighboring water-benzene pairs has revealed that the radius of the first hydration shell of the benzene molecules is independent of the thermodynamic conditions, even if the system consists of one single phase. It has been found that the nearest water neighbors of the benzene molecules are preferentially located above and below the benzene ring, whereas more distant water neighbors, belonging still to the first hydration shell, prefer to stay within the plane of the benzene molecule. In the two-phase systems the dipole vector of the nearest waters has been found to be preferentially perpendicular to the vector pointing from the center of the benzene molecule to the water O atom.     

基于地统计学与支持向量回归的QSAR建模

基于主成分分析(PCA)、地统计学(GS)和支持向量回归(SVR), 提出了一种新的定量构效关系(QSAR)个体化预测方法——Weight-PCA-GS-SVR. 其基本思路是: 先以PCA降维并消除自变量间的信息冗余, 继以SVR经非线性主成分筛选去除与因变量无关的主成分, 再以保留主成分计算样本间的加权距离, 然后以高维GS确定公用变程; 每一个待测样本都以自身为中心从训练集中找出加权距离小于公用变程的私有k个近邻, 以SVR训练建模完成个体化预测. Weight-PCA-GS-SVR从行、列两个方向对模型进行了优化, 为自变量提供了一种新的加权方法, 为解决最优k近邻选择难题提供了新的思路, 并具有SVR原来的优点. 经3个化合物活性实例数据集验证, 新方法在所有参比模型中预测精度最高, 且明显优于文献报道结果, Weight-PCA-GS-SVR在QSAR等回归预测领域有较广泛的应用前景.     

Monte Carlo simulation for the formation of a mixed crystal from two solids in contact

The study focuses on nucleation and growth of a binary mixed crystal phase from two pure crystals in contact. Monte Carlo simulations of this process are conducted, with the dynamics proceeding via activated atom-vacancy exchanges. Intermolecular interactions, ranging up to next-nearest neighbors, are of size typical of hydrogen bonded systems. The process is driven by the formation of strong AB bonds at the expense of weaker AA and BB bonds. In the resulting model, the material is channeled and transported through the mixed phase crust along antiphase boundaries. The flow of molecules through the channels is directed, due to molecular energy lowering via gradual acquisition of an increasing number of nearest neighbors of the second species. On the other hand, defect motion is quasirandom. The model accounts partially for the t(1/alpha) (alpha>3) time dependence observed for conversion of nanoparticles of HBr dihydrate to monohydrate, by exposure to acid adsorbate.     

化学环境编码与分子相似度计算

分子相似度方法主要用于药物分子设计中先导化合物的选取及化合物物理、化学性质的预测,这种方法所依据的原理是：相似的化合物结构将具有相似的化学及物理性质［‘,’1．将已知具有某种性质的化合物的结构（常称为探针化合物）与诸多化合物进行比较,由此得到与之相似的化合物,这种邻近化合物有可能在分子设计中做先导化合物．近年来已报道过多种化合物相似度的计算方法,可粗略的归为以下几类：（l）结构碎片法［‘’‘j;（2）拓扑指数法卜·“;（3）量子化学方法［’,’j．本文提出一种新的化学环境编码方法,该方法有别于结构碎片…     

Stabilities of multiply charged dimers and clusters of fullerenes

The authors find even-odd variations as functions of r (...+[C60]2(r+)([C60C70](r+)) electron-transfer collisions. This even-odd behavior is in sharp contrast to the smooth one for fullerene monomers and may be related to even-odd effects in dimer ionization energies in agreement with results from an electrostatic model. The kinetic energy releases for dimer dissociations [predominantly yielding intact fullerenes [C60]2(r+)-->C60(r1+)+C60(r2+) in the same (r1=r2) or nearby (r1=r2+/-1) charge states] are found to be low in comparison with the corresponding model results indicating that internal excitations of the separating (intact) fullerenes are important. Experimental appearance sizes for the heavier clusters of fullerenes [C60]n(r+) (n>3 and r=2-5) compare well with predictions from a new nearest-neighbor model assuming that r unit charges in [C60]n(r+) are localized to r C60 molecules such that the Coulomb energy of the system is minimized. The system is then taken to be stable if (i) two (singly) charged C60 are not nearest neighbors and (ii) the r C60(+) molecules have binding energies to their neutral nearest neighbors which are larger than the repulsive energies for the (r-1) C60(+)-C60(+) pairs. Essential ingredients in the nearest-neighbor model are cluster geometries and the present results on dimer stabilities.     

ESR and calculations on electronic structure of phenalenyl and phenalenyl derivative radicals

Calculations on electronic structure of the perinaphthenyl radical and phenalenyl derivative radicals responsible for the composition of the ESR spectrum of marine diesel under heating were performed to obtain support for the experimental ESR results. The parameters calculated were the hyperfine coupling constants (A), which were then used for comparison with the experimental data. The energy‐minimized structures were obtained using the density functional theory method. In all cases, the symmetry system was taken into account in theoretical calculations. The differences between experimental and theoretical values were below 7% for nearest hydrogens in molecules, named hyperfine coupling constant A (first neighbors) and 18% for farthest hydrogens atoms named hyperfine coupling constants A′ (second neighbors), for all structures analyzed. Copyright © 2014 John Wiley & Sons, Ltd.     

Alkyl-thiol Langmuir films on the surface of liquid mercury

The coverage dependent phase behavior of monolayers of alkyl thiols (CH3(CH2)(n-1)SH, denoted as CnSH) on mercury was studied for chain lengths 9 相似文献   

Phase diagram of subphtalocyanine ordering on Ag(111)

A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine-Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction-of fourth and fifth, and repulsion-of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.     

On the use of Laplace's equation for global predictions of internuclear separation and dissociation energy

Properties of target species can be estimated by various means including interpolations in periodic charts. Interpolation is equivalent to numerical solution of the Laplace equation. A test of this equivalence, within some confidence level, for any N-atomic molecule surrounded by 4N nearest neighbors: the sum of the second differences of the data in all directions must be zero. Since very few molecules have 4N neighbors with known data, the test becomes: the sum of the averages of the second differences must be zero. The validity of these tests is explored. For radii of main-group atoms, and for internuclear separations of their diatomic combinations, the averages are different from zero and the sums of the averages are zero to within one if second-nearest neighbors are used. Dissociation potentials pass the tests but with larger scatter. Predictions for dissociation potentials, using iterative interpolation within boundaries on which there are known data, are reviewed.     

Photo-induced chirality switching in a cobaloxime complex crystal

Switching of molecular chirality under photo-irradiation was studied in a cobaloxime complex crystal. Excitation of the d-d transition of the Co(III) ion appeared to be much more effective in inducing the chirality change than excitation of the ligand-metal charge transfer band although the latter is more effective in breaking the Co-C bond that initiates the chirality switching. The chirality change versus irradiation time showed a steplike behavior suggesting that chirality switching of molecules occurred in correlation with their nearest neighbors.