Analysis and Simulation of Molecular Dynamics of Lysozyme in Water Cluster System

The influence of water on protein conformation was investigated by simulating the molecular dynamics of a model protein lysozyme in different water systems.The lysozyme-water system with TIP3P water model and lysozyme-water cluster system with six-ring water model were evaluated.In addition,the radial distribution function of solvent around lysozyme was calculated.It is found that the distribution of water molecules around lysozyme is similar to that of water clusters.The analyses of dihedral angles and disulfide bonds of lysozyme show that the conformation of lysozyme is severely damaged in the lysozyme-water cluster system compared with that in the lysozyme-water system.This difference can be attributed to the formation of larger number of intermolecular hydrogen bonds between lysozyme and water cluster.It is in agreement with the analysis that water clusters can change the degree of denaturation in the process of heat denaturation of lysozyme.

Hydrothermal Synthesis,Crystal Structure and Thermal Stability of a Novel Water Cluster [Mn(phen)_2·H_2O·Cl]·p-FBA·3H_2O

A novel water cluster [Mn（phen）2·H2O·Cl]·p-FBA·3H2O （p-FBA = p-fluorobenzoic acid and phen = 1,10-phenanthroline） was synthesized by the hydrothermal reaction of MnCl2 with p-FBA and phen at 150 ℃ and characterized by elemental analysis,IR spectra and TG. Its crystal structure was determined by X-ray single-crystal diffraction study. The crystal belongs to the triclinic system,space group P1,with a = 10.5768（1）,b = 11.5960（1）,c = 12.9916（2） ,α = 101.816（2）,β = 95.397（2）,γ = 103.052（2）o,V = 1502.8（3） 3,Z = 2,Dc = 1.463 g/cm3,R = 0.0399 and wR = 0.0997. The crystal structure shows that the manganese（Ⅱ ） ion is six-coordinated by four nitrogen atoms,one chloride ion and one oxygen atom forming a distorted octahedral coordination geometry. The structure includes three acyclically connected water molecules and one coordinated water molecule thus forming a （H2O）4 water cluster. This water pattern forms a cross-linked discrete ring. The steady （H2O）4 is further extended into a cage-like structure by the hydrogen-bonding interaction formed by dissociative aqua molecule and Cl-ligand. The dimer structure is further extended into a one-dimensional （1D） structure through C-H···O interaction. π···π Stacking interaction among adjacent phen aromatic rings further stabilizes the crystal structure.

MOLECULAR DYNAMICS SIMULATIONS OF FILLED AND EMPTY CAGE-LIKE WATER CLUSTERS IN LIQUID WATER AND THEIR SIGNIFICANCE TO GAS HYDRATE FORMATION MECHANISMS

Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.

A Novel Zn(Ⅱ)Complex with 1D Supramolecular Water Tape Formed by Cyclic Tetrameric Water Clusters

A new mixed-ligand Zn（II） complex, [Zn（4,4′-bipy）2（H2O）4]-2ANS·6H2O （1, 4,4′- bipy = 4,4′-bipyridine, HANS = 2-aminonaphthalene-l-sulfonic acid）, has been isolated and structurally characterized by single-crystal X-ray diffwaction, FT-IR spectrum, TG and elemental analysis. It crystallizes in the monoclinic system, space group P2 1/c with a = 12.4852（8）, b = 18.3163（12）, c = 10.9707（7） A, β = 114.2600（10）°, V= 2287.3（3） A3, Dc = 1.455 g/cm3, Mr = 1002.37, Z = 2, F（000） = 1048,μ = 0.704 mm＂1, the final R = 0.0408 and wR = 0.962 for 4029 observed reflections with I 〉 2σ（I）. Interestingly, an unusual one-dimensional （1D） water tape with cyclic tetrameric water clusters can be observed in 1, which are further trapped via Zn-O coordination bonds exhibiting a 2D Zn（Ⅱ）-water layer. These 2D Zn（Ⅱ）-water layers are stacked together into a 3D interdigitated supramolecular architecture via weak π…π interactions, in which free ANS anions are tightly filled by hydrogen-bonding interactions. Thus, π…π and classical hydrogen-bonding interactions are fotmd as main driving forces to stabilize the 2D Zn（Ⅱ）-water layers.

Effects of Small Water Clusters on the Growth and Microcystin Production of Microcystis aeruginosa

Mierocystis aeruginosa FACHB 905 was used as a model organism to study the ellects oI small water clusters （SWCs） on the growth and microcystin （MC） production of toxic cyanobacteria. The results showed that SWCs were able to stimulate the growth of Microcystis aeruginosa, which resulted in increased cell numbers and higher specific growth rates after a 30-d treatment. The cell morphology indicated that Microcystis aeruginosa was in a better state of growth, and it was more prone to divide in SWCs than in normal water clusters. The SWCs treatment up-regulated MC synthesis and exudation in 10 d in Microcystis aeruginosa, and the intra-cellular MC content de- creased after the 20th day subsequently. Moreover, the cellular photosynthetic pigment contents were temporarily stimulated by SWCs. A possible reason is that SWCs stimulated the growth by promoting photosynthesis, whereas the increased MC production was relevant to pigment contents.

Theoretical Study of Small Water Clusters of Sulfur Dioxide

The intermolecular clusters of sulfur dioxide with water, SO2（H2O）n （n = 2～5）, are studied by using B3LYP density functional theory and MP2 ab initio methods along with the large basis sets （6-311＋＋G（d,p） and aug-cc-pVDZ）. The equilibrium geometries, intermolecular binding energies, and anharmonic frequencies of the clusters are calculated and compared with those of pure water clusters and available experiments. SO2 tends to form cyclic hydrogen-bonded complexes with two or three water molecules. In the larger clusters, however, water molecules begin to retain the structure of pure water clusters and segregate from SO2. Infrared absorption assignments for the small clusters are discussed to resolve a possible incorrect assignment in a recent spectroscopic experiment on the clusters.

Pseudopolyrotaxanes of Cucurbit[6]uril： A Three-Dimensional Network Self-assembled by ClO4（H2O）2 Water Clusters

A pseudorotaxane of cucurbit[6]uril （CB[6]） with guest molecule N,N＇-hexamethylenebis （pyrazinyl perehlorate） （BPHP） was synthesized and characterized by IH NMR spectra, IR, single crystal X-ray diffraction analysis and thermogravimetric analysis. The structure of the pseudorotaxane （CB[6]BPHP） is stabilized by host-guest hydro- gen bonds. Self-assembly of the pseudorotaxane produces infinite one-dimensional and two-dimensional networks with intermolecular hydrogen bonds. In the molecular packing of the CB[6].BPHP, C104（H20）2 water clusters serve as bridges to associate these pseudorotaxanes and form three-dimensional networked pseudopolyrotaxane.

3D Ni(Ⅱ)/Cu(Ⅱ) Supermolecular Frameworks Based on Pyridylamine and Fumarate Co-ligands Containing a Trinodal (4,5,6)-Connected Network and a (H2O)16 Water Cluster

Two new complexes, [Ni（dpypda）（H2O）3].（fum） （l） and [Cu2（dpypda）2（fum）2],-8nH2O （2） （dpypda = N2,N4-di（pyridin-2-yl）pyrimidine-2,4-diamine, fum=fumarate）, have been synthesized and characterized by single-crystal X-ray diffraction. Complex 1 is a discrete unit, exhibiting a （4,5,6）-connected framework formed by hydrogen bonding interactions and electrostatic interactions between flee rum dianions and mononuclear [Ni（dpypda）（H2O）3]2＋ cations. However, in complex 2, two crystallographically independent rum dianions adopt the alternative mode of mixed monodentate bridging and chelating and bis（monodentate） bridging Cu（II） atoms to produce a one-dimensional （ID） infinite zigzag chain. And there are unique （H2O）16 water clusters which consist of one cyclic （H2O）4 tetramer and two cyclic （H2O）5 pentamer with six dangling water molecules in its 3D su- pramolecular framework. Both 1 and 2 are characterized by IR and elemental analysis, and the TG properties were also investigated for 2.

Hydrothermal Synthesis, Structure and Properties of a New Phosphomolybdate Based on Novel [Co（H2O）4（HP2Mo5O23）]8 Anions and [H8（H2O）16]8＋ Water Cluster Cations

A pure inorganic {P2MO5O23}6- based cobalt complex [Hs（H2O）16][Co（H2O）4（HP2Mo5O23）2] with a sandglass4ike shape was synthesized and characterized by means of single-crystal X-ray diffraction, powder X-ray diffraction（PXRD）, infrared spectroscopy（IR）, thermogravimetry/differential scanning calorimetry（TG/DSC）, ultraviolet-visible spectroscopy（UV-Vis） and cyclic voltammogram（CV）. Single-crystal X-ray diffraction analysis reveals that the asymmetric unit of compound 1 consists of a half cobalt ion, one {P2M05O23}6- anion, two coordinated water molecules and eight lattice water molecules. It is especially intriguing to note that two {P2Mo5O23}6- clusters are symmetrical about the Co ion, like a sandglass. And a chair-like water cluster with an unprecedented centrosymmetric [Hs（H2O）16]8＋ can be observed in compound 1. Additionally, the electrochemical and catalytic properties of compound I were also investigated.

Hydrogen Bond Cooperative Effect in Single Cage Water Clusters

In this paper,DFT method was used to study the relative stability of hydrogen bonding networks of numerous 512,51262 and 435663 water cluster isomers.Herein we introduced an optimized six-digit definition to characterize diverse sub-grouped hydrogen bonds to consider the cooperative effect of the nearest and nextnearest neighbor water molecules.There are totally 74 kinds of sub-grouped hydrogen bonds in cage hydrate clusters,and these energies can be obtained by iterative calculations.This improvement effectively explains some regularity contained in hydrogen bonding cooperative effect.In general,donor or acceptor fragment sharing identical value of three independent digits usually performs poor cooperative effect,indicating that the existence of those same-digital-array fragments is the necessary condition to judge poor cooperative effect.Vice versa,the existence of different-digital-array is also the necessary condition to judge strong cooperative effect.

In-situ discrimination of the water cluster size distribution in aqueous solution by ToF-SIMS

The size distribution and molecular structure of water clusters play a critical role in the chemical,biological and atmospheric process.The common experimental study of water clusters in aqueous solution is challenged due to the influence of local H-bonding environments on vibration spectroscopies or vacuum requirements for most mass spectrometry technologies.Here,the time-of-flight secondary ion mass spectrometry（To F-SIMS）combining with a microfluidic chip has been applied to achieve the in-situ discrimination of the size distribution for water clusters in liquid water at room temperature.The results demonstrated that the presented method is highly system stable,reproducible and accurate.The comparison of heavy water with pure water was made to further demonstrate the accuracy of this technique.These results showed that（H2O）3H-＋ and （D2O）4D-＋ are the most dominant clusters in pure and heavy water,respectively.This one water molecule difference in the dominant cluster size may due to the nuclear quantum effects on water’s hydrogen bonded network.It is the first time to experimentally show the size distribution of water clusters over a wide range（n=1–30）for pure

Computer study of the formation of water-ammonia clusters and their dielectric properties

The absorption of one to six ammonia molecules by the （H2O）50 cluster is studied by the molecular dynamics method under near-atmospheric conditions. The capture of NH 3 molecules by a water cluster produces an increase in the integrated intensity of IR absorbance, substantially decreases emission power in the frequency range of 0≤ω≤3500cm-1,and transforms a continuous reflectance spectrum into a banded one. Adsorption of ammonia molecules by water clusters greatly diminishes the number of electrons that are active with respect to electromagnetic radiation. The present results are also compared with the experimental findings wherever available.

Halide-Anion Water Clusters in Cucurbit[6]uril Supramolecular Systems

Three types of dihalide water clusters [X2（H20）8]2 （X=Cl, Br） and [I2（H20）10]^2- have been observed in cucurbit[6]uril supramolecular systems with same guest. According to the single crystal data and the quantitative theory computation, with the increase of electronegativity of halide ions, dihalide water clusters become more stable. A further comparison of three kinds of guests with different molecule length but the same anions, [p-phenylenediamine salt, hexamethylenediamine salt and N,N＇-hexamethylenebis（pyrazinylbromide）], gives the result that the dihalide water clusters collapse from 2D to 1D with the increase of the lengths.

Dimensional effects of organic anion templates in modulating the assembly of water clusters in cucurbit[6]uril supramolecular systems

Two new supramolecular architectures {（HC2O4）2^2- [C6H（18）N2^2＋ C（36）H（36）N（24）O（12）]} 12H2O（1） and{（C6H5SO3）22 [C6H（18）N22＋ C（36）H（36）N（24）O（12）]} 12H2O（2） were synthesized and characterized by singlecrystal X-ray diffraction, thermogravimetric analysis and X-ray powder diffraction. Compound 1contains infinite two dimensional（2D） L18（8）14（8）8（4） type anion–water aggregates [（HC2O4）4（H2O）（22）]^4- and results in the construction of sandwich-like three dimensional（3D） networks. In compound 2, honeycomb-like three dimensional（3D） networks are fabricated by one dimensional（1D）＂W＂-like T5（0）A2 type anion–water clusters [（C6H5SO3）（H2O）6]^-. These results indicate that anionic groups play a crucial role in modulating the structures of water clusters with their spatial structure and binding sites. In these two structures, the majority of interactions are O...H and H...H interactions on the Hirshfeld surface, which means that hydrogen bonding and hydrophobic interactions are the dominate drive forces in forming these supramolecular systems.

Chirality recognition in concerted proton transfer process for prismatic water clusters

Proton transfer and chiral conversion via hydrogen bonds (HBs) are important processes in applications such as chiral recognition, enzymatic catalysis, and drug preparation. Herein, we investigate the chiral conversion and interlayer recognition, via concerted intralayer proton transfer (CIPT) processes, of small prismatic water clusters, in the form of bilayer n−membered water rings (BnWRs, n = 4, 5, 6). Density functional theory (DFT) calculations show that despite the small energy variations between the initial and final states of the clusters of less than 0.3 kcal·mol−1, the vibrational circular dichroism (VCD) spectrum provides clear chiral recognition peaks in the range of 3,000 to 3,500 cm−1. The vibrational modes in this region correspond to stretching of intralayer HBs, which produces strong signals in the infrared (IR) and Raman spectra. The electronic circular dichroism (ECD) spectrum also reveals obvious chiroptical characteristics. The molecular orbitals involved in the interlayer interaction are dominated by O 2p atomic orbitals; the energy of these orbitals increased by up to 0.1 eV as a result of the CIPT processes, indicating corresponding recognition between monolayer water clusters. In addition, isotopic substitution by deuterium in the BnWRs results in characteristic peaks in the VCD spectra that can be used as fingerprints in the identification of the chiral structures. Our findings provide new insights into the mechanism of chiral recognition in small prismatic water clusters at the atomic level as well as incentives for future experimental studies. [Figure not available: see fulltext.] © 2016, Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

Exploration of the Existence Forms and Patterns of Dissolved Oxygen Molecules in Water

The structure of liquid water is primarily composed of three-dimensional networks of water clusters formed by hydrogen bonds,and dis-solved oxygen is one of the most important indicators for assessing water qual-ity.In this work,distilled water with different concentration of dissolved oxygen were prepared,and a clear negative correlation between the size of water clus-ters and dissolved oxygen concentration was observed.Besides,a phenomenon of rapid absorption and release of oxygen at the water interfaces was unveiled,suggesting that oxygen molecules predominantly exist at the interfaces of water clusters.Oxygen molecules can move rapidly through the interfaces among water clusters,allowing dissolved oxygen to quickly reach a saturation level at certain partial pressure of oxygen and temperature.Further exploration into the mechanism by molecular dynamics simulations of oxygen and water clusters found that oxygen molecules can only exist stably at the interfaces among water clusters.A semi-empirical formula relating the average number of water molecules in a cluster(n)to ^(17)O NMR half-peak width(W)was summarized:n=0.1 W+0.85.These findings provide a foundation for exploring the structure and properties of water.

Application of the ABEEM/MM model in studying the properties of the water clusters(H_2O)_n(n=7-10)

ABEEM/MM model has been applied to compute the various properties characterizing water clusters(H2O) n(n = 7-10) ,such as optimized geometries,the hydrogen bonds number,cluster interaction en-ergies,stabilities,ABEEM charge distributions,dipole moments,structural parameters,and so on,and to describe the transition reflected by the hexamer region from two-dimensional(from dimer to pen-tamer) to three-dimensional structures(for clusters larger than the hexamer) .

Projection pursuit cluster model and its application in water quality assessment

One of the difficulties frequently encountered in water quality assessment is that there are many factors and they cannot be assessed according to one factor, all the effect factors associated with water quality must be used. In order to overcome this issues the projection pursuit principle is introduced into water quality assessment, and projection pursuit cluster(PPC) model is developed in this study. The PPC model makes the transition from high dimension to one-dimension. In other words, based on the PPC model, multifactor problem can be converted to one factor problem. The application of PPC model can be divided into four parts: (1) to estimate projection index function Q(); (2) to find the right projection direction ; (3) to calculate projection characteristic value of the i th sample z-i, and (4) to draw comprehensive analysis on the basis of z-i. On the other hand, the empirical formula of cutoff radius R is developed, which is benefit for the model to be used in practice. Finally, a case study of water quality assessment is proposed in this paper. The results showed that the PPC model is reasonable, and it is more objective and less subjective in water quality assessment. It is a new method for multivariate problem comprehensive analysis.

Application of Surface Water Quality Classification Models Using Principal Components Analysis and Cluster Analysis

Water quality monitoring has one of the highest priorities in surface water protection policy. Many variety approaches are being used to interpret and analyze the concealed variables that determine the variance of observed water quality of various source points. A considerable proportion of these approaches are mainly based on statistical methods, multivariate statistical techniques in particular. In the present study, the use of multivariate techniques is required to reduce the large variables number of Nile River water quality upstream Cairo Drinking Water Plants (CDWPs) and determination of relationships among them for easy and robust evaluation. By means of multivariate statistics of principal components analysis (PCA), Fuzzy C-Means (FCM) and K-means algorithm for clustering analysis, this study attempted to determine the major dominant factors responsible for the variations of Nile River water quality upstream Cairo Drinking Water Plants (CDWPs). Furthermore, cluster analysis classified 21 sampling stations into three clusters based on similarities of water quality features. The result of PCA shows that 6 principal components contain the key variables and account for 75.82% of total variance of the study area surface water quality and the dominant water quality parameters were: Conductivity, Iron, Biological Oxygen Demand (BOD), Total Coliform (TC), Ammonia (NH3), and pH. However, the results from both of FCM clustering and K-means algorithm, based on the dominant parameters concentrations, determined 3 cluster groups and produced cluster centers (prototypes). Based on clustering classification, a noted water quality deteriorating as the cluster number increased from 1 to 3. However the cluster grouping can be used to identify the physical, chemical and biological processes creating the variations in the water quality parameters. This study revealed that multivariate analysis techniques, as the extracted water quality dominant parameters and clustered information can be used in reducing the number of sampling parameters on the Nile River in a cost effective and efficient way instead of using a large set of parameters without missing much information. These techniques can be helpful for decision makers to obtain a global view on the water quality in any surface water or other water bodies when analyzing large data sets especially without a priori knowledge about relationships between them.

The cluster analysis of the water masses in western Taiwan Strait from hydrologic And chemical factors

On the basis of mixture theory of concentration of Helland-Hansen (Mao et al, 1964; Helland-Hansen, 1916), this paper takes salinity as a conservative factor in the process of dilution and mixture and selects by relating analysis the bydrological and chemical factors which are closely related to salinity. Then making use of the Q type multi-dimensions cluster analysis, we get the results that the water masses in the western Taiwan Strait include the follying: the coastal water along Fujian, Zhejiang and Guangdong Provinces, the diluted fresh water of Minjiang, Jiulong and Hanjiang Rivers; the mixing water in the Taiwan Strait; upwelling cold/warm water to the northwest of the Taiwan Shoal and the upwelling water to the east of Guangdong. The mixing weter in the Taiwan Strait during spring and summer is composed of a Kuroshio branch, the surface weter of the South China Sea, outal wier along Fujian, Zhejiang and Guangdong Provinces. While in autunm and winter, it is mixed up from Kuroshio branch, the shelf weter in the East China Sea, and the coastal water along Fujian, Zhejiang and Guangdong. There is an obvious seasonal change of growth and decline in these water masses.