Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM

Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.     

Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems

The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics,in which the difficulty is how to reasonably and accurately describe the ion-water and ion-biomolecule interactions.This paper summarizes the development and applications of the atom-bond electronegativity equalization fluctuating charge force field model,ABEEM/MM,in the investigations of ion hydration,metalloproteins and ion-DNA bases systems.Based on high-level quantum chemistry calculations,the parameters were optimized and the molecular potential functions were constructed and applied to studies of structures,activities,energetics,and thermodynamic and kinetic properties of these ion-containing systems.The results show that the performance of ABEEM/MM is generally better than that of the common force fields,and its accuracy can reach or approach that of the high-level ab initio MP2 method.These studies provide a solid basis for further investigations of ion selectivity in biomolecular systems,the structures and properties of metalloproteins and other related ion-containing systems.     

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.     

Microscopic heterogeneity in viscoelastic properties of molecular assembled systems

An important step in understanding molecular assembled systems is to examine the structure and physical properties at various length scales and clarify the correlation between them. However, while the structures of these systems have been extensively studied from nanoscopic to macroscopic scales, their viscoelastic properties have been often limited to bulk rheological measurements. By using optical tweezers and particle tracking, we here show the local viscoelastic properties and their spatial distributions for the following systems: worm-like micelle solution, supramolecular hydrogel and lyotropic liquid crystal, which are formed by self-assembly of amphiphilic molecules in water. We found that all systems studied possessed a spatial heterogeneity in their viscoelastic properties and this was originated from the heterogeneous structures. It is interesting to note that there is the heterogeneity with the characteristic length scale of sub-micrometer or micrometer scale, thereby structures, although the systems are formed by molecules with nanometer size. The findings of these studies should lead to a better understanding of the dynamics of such systems.     

An investigation of crambin and BPTI based on ABEEM/MM model

Molecular dynamics simulation studies on crambin,BPTI(298 K,in vacuo) have been performed by ABEEM/MM method. Some structural properties were discussed.The results show fair consistency with those from X-ray experiment,Moreover, ABEEM/MM model can properly describe the interactions of hydrogen bond of protein systems.     

Molecular Dynamics Simulation on Stability of Insulin on Graphene

The adsorption dynamics of a model protein （the human insulin） onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed Systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Theoretical and Experimental Studies on Photophysical Characteristics of Low Bandgap Polymers

The basic photophysical characteristics of low bandgap polymer poly{2,7＇-9,9-dioctylfluorene-alt-5- diethylhexyl-3,6-bis（5-bromothiophen-2-yl）pyrrolo[3,4-c]pyrrole-1,4-dione}（PDPP-F） have been systematically in- vestigated by means of theoretical and experimental methods. The quantum chemical calculations clarify the molecular structure and electronic transition properties of PDPP-F. The transient absorption data were used to compare the relaxation dynamics of PDPP-F in chlorobenzene and solid film. It is observed that the dynamics process of simulated emission relaxes much faster in comparison with that of excited state absorption in both the solution and solid film. Moreover, the excitation intensity-dependent dynamics of PDPP-F confirms that the interaction among intrachain excitons may occur under photoexcitation in the solution and solid film.     

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.     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

Effects of Non-specific and Specific Solvation on Adsorption of BPTI on Au Surface： Insight from Molecular Dynamics Simulation

Proteins adsorption at solid surfaces are of paramount important for many natural processes. However, the role of specific water in influencing the adsorption process has not been well understood. We used molecular dynamics simulation to study the adsorption of BPTI on Au surface in three water environments （dielectric constant model, partial and full solvation models）. The result shows that a fast and strong adsorption can occur in the dielectric environment, which leads to significant structure changes, as confirmed by great deviation from the crystal structure, largely spreading along the Au surface, rapid lose in all secondary structures and the great number of atoms in contact with the surface. Compared to the dielectric model, slower adsorption and fewer changes in the calculated properties above are observed in the partial solvation system since the specific water layer weakens the adsorption effects. However, in the partial solvation system, the adsorption of polar Au surface causes a significant decrease in the specific hydration around the protein, which still results in large structure changes similar to the dielectric system, but with much less adsorption extent. Enough water molecules in the full solvation system could allow the protein to rotate, and to large extent preserve the protein native structure, thus leading to the slowest and weakest adsorption. On the whole, the effects of non-specific and specific solvation on the protein structure and adsorption dynamics are significantly different, highlighting the importance of the specific water molecule in the protein adsorption.     

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) .     

Characterization and Three-dimensional Structural Modeling of Humic Acid via Molecular Mechanics and Molecular Dynamic Simulation

The humic acid（HA） sample obtained from the alluvial soil was characterized by elemental composition, pyrolysis gas chromatography-mass spectrometry（Py-GC-MS） and solid-state 13C nuclear magnetic resonance （13C NMR） spectroscopy. There is high fat content and a few nitrogen-containing functional groups in HA. Py-GC-MS demonstrates the characterization and structural identification of HA. One long list of identified pyrolysis products was proposed for the construction of conceptual model of HA. Solid-state 13C NMR data indicate there are higher values of alkyl-C, O-alkyl-C and aryl-C in HA. The elemental composition, structural carbon distribution and L3C NMR spectroscopy of simulated HA are consistent with those of experimental HA. HyperChem was used to simulate the three-dimensional molecular structure of the monomer, which was optimized by the molecular mechanics of the optimized potential for liquid simulations（OPLS） force field and molecular dynamics simulation to get the stable and balanced conformation. The deprotonation process study depicts that the degree of ionization of HA gets deeper, while the electronegativity of HA and the energy of van der Waals（vdW） increase. Moreover, the 3D structure of humic acid with -4 charges is the most stable. The deprotonation process is an endothermic process.     

Insight into the Urea Binding and K166R Mutation Stabilizing Mechanism of TIpB： Molecular Dynamics and Principal Component Analysis Study

Chemoreceptor TlpB（Tlp=transducer-like protein）, which has been demonstrated to respond to pH sensing function, is crucial for the survival ofHelicobacterpylori（H, pylori） in host stomach. Urea was proposed to be essen- tial for TlpB＇s pH sensing function via binding with the Per-ARNT-Sim（PAS） domain of TlpB. Additionally, KI66R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Al- though X-ray crystallographic studies have been carried out for urea-bound Tlpl3, the molecular mechanism for the stabilization of TIpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis（PCA） for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Aspll4, which were induced by both urea binding and K166R mutation of TIpB, were im- portant to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may Dave the wav for the further researches of TlpB.     

Molecular dynamics study of the water/n-alkane interface

Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference ...     

Preconcentration and Determination of Trace Amounts of Heavy Metals in Water Samples Using Membrane Disk and Flame Atomic Absorption Spectrometry

A fast and simple method for preconcentration of Ni^2＋, Cd^2＋, Pb^2＋, Zn^2＋, Cu^2＋ and Co^2＋ from natural water samples was developed. The metal ions were complexed with sodium diethyldithiocarbamate （Na-DDTC）, then adsorbed onto octadecyl silica membrane disk, recovered and determined by FAAS. Extraction efficiency, influence of sample volume and eluent flow rates, effects of pH, amount of Na-DDTC, nature and amount of eluent for elution of metal ions from membrane disk, break through volume and limit of detection have been evaluated. The effect of foreign ions on the percent recovery of heavy metal ions has also been studied. The limit of detection of the proposed method for Ni^2＋, Cd^2＋, Pb^2＋, Zn^2＋, Cu^2＋ and Co^2＋was found to be 2.03, 0.47, 3.13, 0.44, 1.24 and 2.05 ng·mL^-1, respectively. The proposed （DDTC） method has been successfully applied to the recovery and determination of heavy metal ions in different water samples.     

Mean Residence Time of CO2 Molecules in Flexible ZIF-8 Cages Explored by Molecular Dynamics Simulations

The adsorption sites and diffusion mechanism of CO2 molecules in the flexible Zn（MeIM）2 （MeIM=2-methylimidazole） （ZIF-8） have been investigated by grand canonical Monte Carlo and molecular dynamics simulations. A reasonable time correlation function is for the first time constructed to explore the mean residence time of CO2 molecules in the ZIF-8 cages, suggesting that C02 molecules can remain in the same cage for up to several tens of picoseconds. Furthermore, we find that the mean residence time almost linearly increases with the increasing pressure （or loading） at 273 and 298 K.     

Understanding the interactions between tris(pentafluoroethyl)-trifluorophosphate-based ionic liquid and small molecules from molecular dynamics simulation

Tris(pentafluoroethyl)trifluorophosphate ([FEP])-based ionic liquids have been widely applied in many fields. For better understanding the properties of [FEP]-based ionic liquids, the interactions between 1-hexyl-3-methylimidazolium ([hmim])[FEP] and small molecules were investigated by molecular dynamics simulations in this work. The small molecules are water, methanol and dimethyl ether. The united-atom (UA) force fields were proposed for methanol and dimethyl ether based on AMBER force field. The densities, enthalpies of vaporization, excess molar properties, and diffusion coefficients of the mixtures were calculated, as well as the microscopic structures characterized by radial distribution functions. Both of the results of the excess energies and microscopic properties show that the strongest interaction is between [hmim][FEP] and dimethyl ether, whereas the interaction between [hmim][FEP] and water is the weakest. Moreover, [hmim][FEP] is more hydrophobic than [hmim] hexafluorophosphate ([PF6]), and the three solutes are mainly distributed around [FEP] anion.     

Modeling phase equilibria of semiclathrate hydrates of CH_4,CO_2 and N_2 in aqueous solution of tetra-n-butyl ammonium bromide

Semiclathrate hydrates of tetra-n-butyl ammonium bromide(TBAB) offer potential solution for gas storage,transportation,separation of flue gases and CO2 sequestration.Models for phase equilibria for these systems have not yet been developed in open literatures and thus require urgent attention.In this work,the first attempt has been made to model phase equilibria of semiclathrate hydrates of CH4,CO2 and N2 in aqueous solution of TBAB.A thermodynamic model for gas hydrate system as proposed by Chen and Guo has been extended for semiclathrate hydrates of gases in aqueous solution of TBAB.A correlation for the activity of water relating to the system temperature,concentration of TBAB in the system and the nature of guest gas molecule has been proposed.The model results have been validated against available experimental data on phase equilibria of semiclathrate hydrate systems of aqueous TBAB with different gases as guest molecule.The extended Chen and Guo's model is found to be suitable to explain the promotion effect of TBAB for the studied gaseous system such as,methane,carbon dioxide and nitrogen as a guest molecule.Additionally,a correlation for the increase in equilibrium formation temperature(hydrate promotion temperature,ΔTp) of semiclathrate hydrate system with respect to pure gas hydrate system has been developed and applied to semiclathrate hydrate of TBAB with several gases as guest molecules.The developed correlation is found to predict the promotion effect satisfactorily for the system studied.