A potential model for the study of ices and amorphous water: TIP4P/Ice

The ability of several water models to predict the properties of ices is discussed. The emphasis is put on the results for the densities and the coexistence curves between the different ice forms. It is concluded that none of the most commonly used rigid models is satisfactory. A new model specifically designed to cope with solid-phase properties is proposed. The parameters have been obtained by fitting the equation of state and selected points of the melting lines and of the coexistence lines involving different ice forms. The phase diagram is then calculated for the new potential. The predicted melting temperature of hexagonal ice (Ih) at 1 bar is 272.2 K. This excellent value does not imply a deterioration of the rest of the properties. In fact, the predictions for both the densities and the coexistence curves are better than for TIP4P, which previously yielded the best estimations of the ice properties.     

Monte Carlo simulation of the local ordering of water molecules. I. Binary spatial correlations

The pair distribution functions (DFs) of the oxygen and hydrogen atoms over space around one of the water molecules were calculated during Monte Carlo simulation (Metropolis procedure for the NVT ensemble at normal density and 300 K). An analysis of the isosurfaces of the DF_OO and DF_OH constructed around the selected water molecule for several fixed values of local density allowed us to obtain detailed information about the most probable localization of water molecules in the second and third coordination spheres.     

A molecular dynamics study of water nucleation using the TIP4P/2005 model

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nose?-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.     

Hydrogen bonding contribution to the water pair interaction potential: Effects on the model liquid structure

Empirical pair potentials of water that take into account the contribution of the OH nonelectrostatic interaction in the hydrogen bond are considered. The effects of this contribution on the radial distribution functions derived by computer simulation are analyzed. Model potentials have been obtained for which the height and position of the first and second peaks of the oxygen-oxygen radial distribution function are comparable with experimental data.Original Russian Text Copyright © 2004 by A. V. Borovkov, M. L. Antipova, V. E. Petrenko, and Yu. M. KesslerTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 678–682, July–August, 2004.Deceased.This revised version was published online in April 2005 with a corrected cover date.     

Principal component analysis versus fuzzy principal component analysis A case study: the quality of danube water (1985-1996)

Principal component analysis (PCA) is a favorite tool in environmetrics for data compression and information extraction. PCA finds linear combinations of the original measurement variables that describe the significant variations in the data. However, it is well-known that PCA, as with any other multivariate statistical method, is sensitive to outliers, missing data, and poor linear correlation between variables due to poorly distributed variables. As a result data transformations have a large impact upon PCA. In this regard one of the most powerful approach to improve PCA appears to be the fuzzification of the matrix data, thus diminishing the influence of the outliers. In this paper we discuss and apply a robust fuzzy PCA algorithm (FPCA). The efficiency of the new algorithm is illustrated on a data set concerning the water quality of the Danube River for a period of 11 consecutive years. Considering, for example, a two component model, FPCA accounts for 91.7% of the total variance and PCA accounts only for 39.8%. Much more, PCA showed only a partial separation of the variables and no separation of scores (samples) onto the plane described by the first two principal components, whereas a much sharper differentiation of the variables and scores is observed when FPCA is applied.     

Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.     

A diagnostic tool for determining the quality of accuracy validation. Assessing the method for determination of nitrate in drinking water

Realistic internal validation of a method implies the performance validation experiments under intermediate precision conditions. The validation results can be organized in an X _Nr×Ns (replicates×runs) data matrix, analysis of which enables assessment of the accuracy of the method. By means of Monte Carlo simulation, uncertainty in the estimates of bias and precision can be assessed. A bivariate plot is presented for assessing whether the uncertainty intervals for the bias (E ± U(E)) and intermediate precision (RSDi ± U(RSDi) are included in prefixed limits (requirements for the method). As a case study, a method for determining the concentration of nitrate in drinking water at the official level set by 98/83/EC Directive is assessed by use of the proposed plot.     

Monte Carlo simulation for the adsorption of symmetric triblock copolymers I. Configuration distribution and density profiles of adsorbed chains

Monte Carlo simulations for the adsorption of symmetric triblock copolymers from a nonselective solvent at a solid-liquid interface have been performed on a lattice model. In simulations, triblock copolymer molecules are modeled as self-avoiding linear chains composed of m segments of A and n segments of B arranged as A_m/2B_nA_m/2. Either segment A or segment B is attractive, while the other is non-attractive to the surface. The microstructure of the adsorbed layers, including the segment-density profiles and the size distribution of loops, tails and trains are presented. The effect of the adsorption energy, the bulk concentration, the chain composition, as well as the chain length on various adsorption properties has been studied. The results have shown that the size distribution of various configurations is dependent of the adsorption energy, the chain composition and the chain length. The mean length of the loops, trains and tails is insensitive to the bulk concentration. The mean length of the trains increases and that of the tails decreases as the adsorption energy and the length of the attractive segments increase. The mean length of the loops for the end-adsorbed copolymers appears a maximum and that for middle-adsorbed copolymers appears a minimum as the length of attractive segments increases. The length of the non-attractive segments affects mostly the size distribution of the tails. The longer the chain is, the larger the tail appears. The mean length of the tails and loops increases linearly as the length of the non-attractive segments increases, but that of the trains approximately is unchanged.     

A Monte Carlo study of the coil-to-globule transition of model polymer chains near an attractive surface

When a polymer chain in solution interacts with an atomically smooth solid substrate, its conformational properties are strongly modified and deviate substantially from those of chains in bulk. In this work, the interplay of two competing transitions that affect the conformations of polymer chains near an energetically attractive surface is studied by means of Monte Carlo simulations on a cubic lattice. The transition from an extended to a compact conformation of a polymer chain near an attractive wall, as solubility deteriorates, exhibits characteristics akin to the “coil-to-globule” transition in bulk. An effective θ-temperature is determined. Its role as the transition point is confirmed in a variety of ways. The nature of the coil-to-compact transition is not qualitatively different from that in the bulk. Adsorbed polymer chains may assume “globular” or “pancake” configurations depending on the competition among adsorption strength, cohesive energy, and entropy. In a very relevant range of conditions, the dependence of the adsorbate thickness on chain-length is intermediate between that of 3-d (“semidroplets”) and 2-d (“pancake”) objects. The focus of this study is on rather long polymer chains. Several crucial features of the transitions of the adsorbed chains are N-dependent and various aspects of the adsorption and “dissolution” process are manifested clearly only at the “long chain” limit. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2462–2476, 2009     

合成甲醇Cu基催化剂结构敏感性的模拟

运用BOC-MP方法对Cu（111）、Cu（110）上CO2＋H2合成甲醇的甲酸基机理中的可能基元反应步骤的动力学参数进行了计算．在此基础上，结合MonteCarlo模拟技术对该反应过程进行了随机模拟．模拟结果表明，该反应在钢的两种不同单晶表面上的反应活化能值非常接近（其比值为1：1.2，基本吻合于实验值），表明该反应活性与催化剂表面原子排布的关系不甚紧密，即该反应为一非结构敏感反应．     

Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach

Adsorption of protons on a heterogeneous solid surface is modeled using the Monte Carlo (MC) simulation method. The surface of an oxide is assumed to consist of adsorption sites with pK assigned according to a quasi-Gaussian distribution. The influence of the electrostatic interactions combined with the energetic heterogeneity of the surface is examined and the MC results are compared with the predictions of the analytical 1-pK approach. The surface potential behavior is examined using both "experimental" MC results and "theoretical" results obtained from the application of 1-pK model. The results are compared qualitatively with experimental determination of the surface potential of metal oxide surfaces. They confirm that the relation between the surface potential and the pH of bulk solution should not be described by the Nernst equation but by the equation with the parameter linearly reducing Nerstian potential. The values of this parameter are examined with respect to degree of surface energetic heterogeneity and site density of the surface.     

Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system

A periodic reaction field (PRF) method is a technique to estimate long‐range interactions. The method has the potential to effectively reduce the computational cost while maintaining adequate accuracy. We performed molecular dynamics (MD) simulations of a model liquid‐crystal system to assess the accuracy of some variations of the PRF method in low‐charge‐density systems. All the methods had adequate accuracy compared with the results of the particle mesh Ewald (PME) method, except for a few simulation conditions. Furthermore, in all of the simulation conditions, one of the PRF methods had the same accuracy as the PME method. © 2015 Wiley Periodicals, Inc.     

Structure of the HOOO radical in liquid water: a theoretical study.

The HOOO radical is supposed to play a role in ozone chemistry, both in the gas phase and aqueous media. We discuss the influence of the solvent on the electronic and geometrical structure of this radical using density functional and high-level ab initio calculations together with continuum, discrete, and discrete-continuum solvent models. Solute-solvent electrostatic interactions are shown to be fundamental, and lead to a noticeable stabilization of the radical, which should adopt a trans conformation in aqueous media. In fact, no energy minimum for the cis conformation is predicted in these conditions.     

Charged-cell periodic DFT simulations via an impurity model based on density embedding: Application to the ionization potential of liquid water

Calculations of charged systems in periodic boundary conditions (PBC) are problematic because there are spurious interactions between the charges in different periodic images that can affect the physical picture. In addition, the intuitive limit of Coulomb interactions decaying to zero as the interacting charges are placed at infinite separation no longer applies, and for example total energies become undefined. Leveraging subsystem density functional theory (also known as density embedding) we define an impurity model that embeds a finite neutral or charged subsystem within an extended (infinite) surrounding subsystem. The combination of the impurity model and a consistent choice of the Coulomb reference provides us with an algorithm for evaluating the ionization potential (IP) in extended systems. We demonstrate our approach in a pilot calculation of the IP of liquid water, based on a configuration from a prior ab initio molecular dynamics (AIMD) simulation of liquid water (Genova et al., J. Chem. Phys. 2016, 144, 234105). The calculations with the impurity model capture the broadening on the ionization energies introduced by the interactions between the water molecules. Furthermore, the calculated average IP value (10.5 eV) compare favorably to experiments (9.9-10.06 eV) and very recent simulations based on the GW approximation (10.55 eV), while at the same time outperforming density embedding calculations carried out with a naïve handling of the electrostatic interactions (about 7 eV).     

Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Chemometric study and optimization of extraction parameters in single-drop microextraction for the determination of multiclass pesticide residues in grapes and apples by gas chromatography mass spectrometry

A simple and rapid single-drop microextraction method coupled with gas chromatography and mass spectrometry (SDME–GC/MS) for the determination of 20 pesticides with different physicochemical properties in grapes and apples was optimized by the use of a multivariate strategy. Emphasis on the optimization study was given to the role of ionic strength, sugar concentration and pH of the donor sample solution prepared from the fruit samples. Since all three variables were found to affect negatively SDME (a lower extraction efficiency was observed as the values of variables were increased for most of the pesticides studied), donor sample solution was optimized using a central composite design to evaluate the optimum pH value and the optimum dilution of the sample extract. With some exceptions (chlorpyrifos ethyl, α-endosulfan, β-endosulfan, pyriproxyfen, λ-cyhalothrin and bifenthrin), the optimum method included the dilution of the analytical sample by 12.5-fold with a buffered acetone/water solution at pH = 4 and exhibited good analytical characteristics for the majority of target analytes (pyrimethanil, pirimicarb, metribuzin, vinclozolin, fosthiazate, procymidone, fludioxonil, kresoxim methyl, endosulfan sulfate, fenhexamid, iprodione, phosalone, indoxacarb and azoxystrobin) by providing high enrichment factors (14–328), low limits of detection (0.0003–0.007 μg/g), and good precision (relative standard deviations below 15%).     

Development of a generic flow-injection analysis method for compounds with a secondary amine or amide function, using an experimental design approach: Part II. Selection and evaluation of the chemical reaction parameters

A second part in the development of a generic flow injection analysis (FIA) method to determine compounds with a secondary amine or amide in their structure is described. This part consists in the selection and evaluation of the chemical reaction conditions. Sodium hypochlorite first converts the secondary amine or the amide to a primary amine. The latter reacts with o-phthalaldehyde (OPA) and a thiol (N-acetylcysteine (NAC)) to form a derivative which can be measured fluorimetrically. To investigate the influence of the different chemical reaction parameters on the peak height for a set of 31 pharmaceutical compounds, a quarter-fraction factorial design for six factors at two levels (2^6-2-resolution IV, 16 experiments) was executed. Effects on the responses were calculated for each compound. Parallel coordinate geometry (PCG) plots and principal component analysis (PCA) were also applied on the measured responses as aids in the interpretation of the results.     

Chemometric study of the aggregation of alcohol dehydrogenase and its suppression by beta-caseins: a mechanistic perspective

Molecular chaperones interact preferentially with certain aggregation-prone intermediates of target protein molecules. An estimation of the chaperone activity based on suppression of aggregation is required to be mechanistically understood. In this study, the multivariate curve resolution chemometric technique was applied on horse alcohol dehydrogenase (ADH) UV-spectra under thermal stress, to obtain the required information about the number and change in concentrations of the species involved. Chemometric analysis of UV-absorption spectra of horse ADH under thermal stress, led to the existence of three different molecular species including native (N), aggregation-prone intermediate (I) and final aggregate (A) species. Appearance and buildup of two molecular species I and A were connected to the disappearance of N-species. In the presence of β-caseins (BCN), however, a new complex between I and BCN (I-BCN) was formed. Meanwhile, by accretion of concentration of I-BCN complex, the light scattering intensity diminished. The data presented in this study clearly demonstrate that the interaction of BCN as a chaperone molecule with I-species takes place in a temperature-dependent manner and leads to a reversible I-BCN complex. In the absence of chaperones, I-state is subsequently converted to the final aggregate species. In the presence of BCN, this molecular species could be converted to the final aggregate state and/or form the I-BCN complex.     

DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water

Density functional theory (DFT) and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques have been used to study the tautomeric proton transfer reaction of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. Two reaction pathways were considered: the direct and water-assisted transfers. The optimized structures and thermodynamic properties of stationary points for the title reaction system in the gas phase were calculated at the B3LYP/6-311+G(d, p) level of theory. The potential energy profiles along the minimum energy path in the gas phase and in water were obtained. The study of the solvent effect of water on the proton transfer of 2-amino-2-oxozoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline indicates that water as a solvent is favorable for the water-assisted process and slows down the rate of the direct transfer pathway.