A preliminary spectroscopic investigation on the molecular interaction of metal-diphenylthiocarbazone complex with cellulose biopolymer and its application

Biopolymer adsorbents are versatile in their application for removal of heavy metals. The present work is focused towards the preliminary study of the interaction of diphenylthiocarbazone (DTZ) complex of chromium(VI) in acidic medium with cellulose biopolymer. Chromium-DTZ complex could be quantitatively adsorbed on a cellulose column in the pH range 1.0-2.5 and the effect of various experimental parameters such as stability of the column and the complex, column breakthrough volume, and interfering ions have been studied in detail. The probable mechanism of adsorption of complex on the cellulose biopolymer was corroborated using Fourier transform infra-red spectroscopy (FT-IR), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) and solid state 13C nuclear magnetic resonance techniques (CP-MAS). The pores formed due to the hydrogen bond between the cellulose layers and then the ensuing occupation of the complex between these layers and on the surface of the biopolymer layer through electrostatic attractive force and Π interaction of aromatic ring with cellulose are expected to play a vital role in the interaction. The cellulose column could be regenerated using environmentally benign polyethylene glycol-400 (PEG-400) in acidic medium. The cellulose biosorbent has been successfully tested to study the removal of chromium as its dithizone complex from synthetic and real waste water samples.     

A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer

A series of molecular dynamics simulations of dimyristoylphosphatidylcholine bilayers, with different levels of hydration and temperature, were performed to examine the influence of hydration on properties of lipid membranes. Structural and dynamical properties such as area per lipid, electron densities, order parameters for all CH bonds and water, diffusion, and reorientation autocorrelation functions were determined and were all found to be affected by changes in the hydration level. The simulations give an overall picture of the bilayer going to a more ordered state when the hydration level is reduced. Lipid headgroups were found to adopt an orientation more parallel to the membrane plane when the water content was decreased. Dynamical properties such as lipid diffusion and relaxation of reorientation time correlation functions were found to become slower with the removal of water. Our simulation results generally agree with experimental data in cases where such data are available. One important conclusion drawn is that while structural properties are affected only moderately dynamical properties are affected very strongly by a decrease of water content.     

A molecular dynamics study of human endostatin and its synthetic fragments with antiangiogenic properties

Human endostatin is one of the better characterized endogenous angiogenesis inhibitors, and its ability to modulate vascularization of tumours could be of great therapeutic interest. These properties are not exclusive to the full-length protein, but are shared by some of its synthetic fragments. A number of research groups have partitioned human endostatin in different peptides and have investigated their activity, in order to collect a body of experimental data which could be important in shedding new light on their structure-activity relationships. It was also reported that a small active fragment can become inactive when contained in a larger fragment, revealing an apparent discrepancy in the experimental results. Very few studies have been devoted to the computational analysis of these systems and to the rationalization of their properties using molecular modelling. Through molecular dynamics simulations of human endostatin and of four synthetic fragments, we have been able to rationalize the experimental findings. In particular, we have identified a pattern consisting of six amino acids, namely R-R(G)-A-D-R-A, which appears to be an active epitope if it is properly exposed to the solvent. Interestingly, this pattern can be already present in sequential order in the primary structure, or it can be generated by the spatial approach of two groups of residues, far apart in the primary structure, as an effect of the peptide folding. Comparing the structural features and the time evolution of all the simulated peptides we provide a coherent explanation of their activity or inactivity.     

A molecular dynamics investigation of the titration of a trivalent aqueous ion

We carried out a series of molecular dynamics simulations of the hydrolysis of a model trivalent metal ion in aqueous solution. We use a dissociative model for water and examine the spontaneous speciation of M³⁺ into M(OH) _n ^(3-n)+ (n =1,4) both in neutral solution and as a function of added protons and hydroxide ions. The species distributions in neutral solution correspond reasonably well with those expected for real trivalent metal ions at neutral pH. However, the change in the species distributions as a function of either added protons or hydroxide ions is much less than expected with very large concentrations of protons or hydroxide ions required to shift the species equilibria in either direction. The influence of added protons and hydroxide ions on the species distributions appears to be proportional to the average charge of the hydrolysis couples, being highest for the 3+/2+ couple and lowest for the 1+/0 and 0/1- couples. Proton exchange rates vary with proton/hydroxide ion concentration giving a minimum at intermediate values ([H+]≈ 0.166) with increasing rates at both lower and higher pH.     

Atomic-scale investigation of the interaction between coniferyl alcohol and laccase for lignin degradation using molecular dynamics simulations and spectroscopy

The interaction between coniferyl alcohol (CA) and laccase (LAC) was investigated using molecular dynamics (MD) simulations and spectral experiments. The mode of interaction between CA and LAC was established by MD simulations. The micro-environmental changes, stability and rigidity of the LAC-CA system were assessed by relevant parameters. These parameters include root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg). The calculated binding free energy (ΔG_binding=??19.99?kcal·mol.^?1), the van der waals (VDW) contribution (ΔG_vdw=?23.99?kcal·mol^?1) and the electrostatic energy (ΔG_ele=?23.09?kcal·mol^?1) of LAC-CA system demonstrated that the interaction of LAC-CA was a spontaneous process and the main interaction forces were van der Waal's and electrostatic forces. The values of ΔG_vdw and ΔG_ele were negative, which demonstrated that VDW interactions and electrostatic interactions were favorable for the binding of CA and LAC. The binding constants, thermodynamic parameters, molecular force types and binding distances confirmed the interaction between CA and LAC and further verified the rationality of the theoretical model by spectral experiments. The MD simulations and experimental approaches provide clues for the discovery of new mediators and useful references for the mechanism of microbial degradation of lignin and industrialization of lignocellulose.     

Pt-Au合金团簇热力学性质分子动力学模拟研究

采用分子动力学方法和原子嵌入法模型势模拟了Pt原子和Au原子合金纳米团簇的熔化过程,研究了这些金属原子纳米团簇熔点与团簇组分的关系,发现不同组分纳米团簇的熔点不是单调变化的,同时均出现了负热容现象.通过对各种团簇溶化前后结构的比较研究,分析了导致这种现象的原因.     

Lattice dynamics and interaction potentials in molecular crystals

This paper, based essentially on the work done in recent years in our laboratory, presents a critical analysis of harmonic and anharmonic calculations of crystal vibrations in the determination of intermolecular potentials. The main purpose is to show that the dynamical properties are specifically sensitive to different terms of the potential and thus that information extracted from vibrational spectra of crystals is of the greatest importance for the theory of intermolecular forces. The most important conclusion is that these calculations point to the development of anisotropic short-range potentials and orient future researches towards the more complex and elaborate anharmonic treatment of crystal vibrations.     

A molecular dynamics investigation of hydrolytic polymerization in a metal-hydroxide gel

The early stages of the spontaneous hydrolytic polymerization of an active hydroxide in the anti-bayerite structure are followed by using molecular dynamics simulations. The polymer populations are calculated as a function of reaction progress and compared with a model governed by purely random bonding. In agreement with experimental observations in aqueous solutions, the transformation of singly bridged to doubly bridged metal ions is shown to have a significant autocatalytic component. The overall polymer populations, however, are very close to the predictions of the random bonding model, indicating that local autocatalytic behavior is decoupled from multimer populations at the larger scales. The calculations show that solid-state transformation processes do not preferentially give rise to higher order multimers, and suggest that interfacial processes, involving bulk solution, are required to facilitate rapid transformation to higher order oligomers. Two reaction pathways are identified for the dewatering of mu-H(3)O(2) bridges into mu-OH bridges. Both are activated primarily by undercoordination of one of the metals centers involved in the bridge.     

The electrostatical molecular potential — A tool for the prediction of electrostatic molecular interaction properties

Starting from the molecular potential we get, by using elementary electrostatics, information about energetically favoured regions for interaction with ions and dipoles around H₂O and H₂CO. The molecule-dipole interaction is represented by the electric field patterns.     

A molecular dynamics investigation of the structural and dynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide

Molecular dynamics simulations have been performed to investigate the structure and dynamics of the ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C(4)mim][Tf(2)N]) in the temperature range of 283-460 K. Extensive analysis was carried out to characterize a number of structural and dynamic features. Transport properties were computed using a variety of equilibrium methods that employed the Green-Kubo and Einstein formulations. Nonequilibrium techniques were also used. In general, different methods mostly yielded consistent results, although some differences were observed. Computed self-diffusivities and ionic conductivities tended to be slightly lower than experimental values, while computed viscosities were significantly higher than experiment. Computed thermal conductivities agreed reasonably well with experimental data. Despite these discrepancies, the simulations capture the experimental temperature-dependent trends for all these transport properties. Single ion dynamics were studied by examining diffusional anisotropy, the self-part of the van Hove function, non-Gaussian parameters, and incoherent intermediate scattering functions. It is found that cations diffuse faster than anions and are more dynamically heterogeneous. A clear anisotropy is revealed in cation displacement, with the motion normal to the imidazolium ring plane being the most hindered and the motion along the alkyl chain in the plane of the ring being the most facile. Cations structurally relax faster than anions but they rotationally relax slower than anions. There is a pronounced temperature dependence to the rotational anisotropy of the cations, but only a weak temperature dependence for the anions. The ionic conductivity deviates from the Nernst-Einstein relation due to the correlated motion of cations and anions. The results suggest that the dynamical behavior of this and related ionic liquids is extremely complex and consists of many different modes with widely varying timescales, making the prediction of dynamical trends extremely difficult.     

Exploring the possibilities to control the molecular switching properties and dynamics: A field-switchable rotor-stator molecular system

A bistable, dipolar stator-rotor molecular system-candidate for molecular electronics is investigated. We demonstrate that it is possible to control the intramolecular torsional states and dynamics in this system by applying an appropriate additional electric field (instead of biasing one), achieving fine tuning and modulation of the relevant properties. The electric field effects on the quantities responsible for torsional dynamics (potential energy surface, potential barrier height, quantum and classical transition probabilities, correlation time, HOMO-LUMO gap) are studied from first principles. Our results indicate that it is possible to artificially stabilize the metastable conformational state of the studied molecule. The importance of this is evident, as the current-voltage characteristics of the metastable state are clearly distinguishable from the current-voltage characteristics of the two stable states. We report for the first time exact calculations related to the possibilities to control the thermally induced stochastic switching, and reduce the noise in a practical application. Thus, we believe that the molecule studied in this paper could operate as a field-switchable molecular device under real conditions.     

Theoretical investigation of polymer molecular structure influence on dielectric properties and mechanical properties

Triboelectric nanogenerator (TENG) technologies have explosive development in the field of energy harvesting and self-powered sensing. As the key element of triboelectric devices, dielectric polymers have obtained much attention in recent years. The dielectric properties of polymer determine the output performance of TENG. In this paper, we take silicone rubber as an example of dielectric polymers, to study the properties of molecular structure influence on the dielectric properties and mechanical properties by the molecular dynamics simulation method. The free volume fraction, dielectric constant, and mechanical properties of silicone rubbers with different branch chains were calculated. The dielectric constant is highly related to the free volume distribution and the dipole moments of silicone rubbers with different amounts of branch chains. For fewer branch chains silicone rubber, the free volume distribution contributes most to the dielectric constant; for more branch chains silicone rubber, the dipole moment dominates the dielectric constant. Therefore, the silicone rubber ratio has a great influence on the dielectric constant of silicone rubber. With the increase of temperature, the dielectric constant of 2-chain silicone rubber increases at first and then decreases, and the maximum value is obtained near 300 K. Therefore, it is necessary to control the temperature when silicone rubber is used as a dielectric material. This work can be a guide for improving the dielectric properties of silicone rubber, and it provides a new approach to the optimal design of high-performance triboelectric nanogenerators.     

Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water

Atomistic molecular dynamics simulations were carried out to obtain information on the rheological, aggregation and disintegration properties of carboxylated (TEMPO-oxidized) cellulose nanofibrils with different functionalization levels. The magnitude of the inter-fibril interaction was quantified for parallel nanofibrils using the umbrella sampling method. The obtained potential of mean force was found highly sensitive to the charge configuration for intermediate functionalization levels. This feature was further studied with an electrostatic model for similar charge configurations and system periodicity as in the case of the molecular dynamics simulations. The electrostatic contribution of the charged surfaces varied from repulsive to attractive depending on the distribution of the carboxylate groups and nearby counter-ions, as well as the distance between the fibrils. The simulated deviations from average behavior for single fibrils in both models suggest heterogeneity in their aggregation and disintegration behavior. This was seen in disintegration experiments, where the differences in disintegration energy and in the structural variation qualitatively agreed with the model predictions. As to aggregation behavior, the studied case with parallel fibrils reflects the upper boundary of the repulsive interaction.     

Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation

A molecular dynamics (MD) simulation study has been carried out to understand the stability of the triple helical collagen models. The calculations show that the presence of the aspartic acid residue in different positions leads to the local variation in the structure. Analyses of root-mean-square deviation (RMSD), radial distribution function (RDF), puckering effect, dihedral angle variation, hydrogen bond (H-bond), and conformational changes during molecular dynamics simulation reveal that the local perturbation in the sequences, increase in chain flexibility due to removal of five membered rings in the collagen by aspartic acid, change of intermolecular H-bonding pattern, and differences in the association of water are mainly influencing the nature of stabilization of collagen by aspartic acid.     

Molecular dynamics investigation of the interaction between IR radiation and an ammonia-water medium

The frequency dependence of the absorption factor and refractive index of a dispersion water system absorbing ammonia are studied by means of molecular dynamics. It is found that the capture of the ammonia molecules by water clusters is accompanied by a substantial reduction in their ability to absorb IR radiation in the frequency range 0 ≤ ω ≤ 3500 cm^?1, and the refractive index of the ammonia-water system of clusters is lowered. It is shown that the maxima of the absorption spectra and the refractive index shift to higher frequencies. Starting from a certain concentration of ammonia in the clusters, however, the integral intensity of the spectra increases.     

含B-N相互作用偶氮苯强荧光材料光电性质的理论研究

本文基于增大光谱发光强度的结构修饰方法,采用理论计算方法研究了结构修饰后分子的电子性质、光谱性质以及电荷传输性质的变化.计算结果表明,-N(CH3)2取代、-N(CH3)2和-Br组合取代有助于吸收/发射光谱发光强度的提高.与母体分子相比,-N(CH3)2和-Br取代位置不同或取代数量不同可以引起最高占据分子轨道能量(EHOMO)、最低空分子轨道能量(ELUMO)和能隙(Eg=ELUMO-EHOMO)发生明显变化,从而有效调节了最大吸收波长(λabs)和最大发射波长(λem),从理论角度设计了一系列蓝光和绿光材料.重组能计算显示,除了GM-1和GM-6,其余分子可以作为有机电致发光材料(OLEDs)中的空穴传输材料,GM-1和GM-7可以作为双极性电荷传输材料.     

Uranyl and strontium salt solvation in room-temperature ionic liquids. A molecular dynamics investigation

Using molecular dynamics simulations, we compare the solvation of uranyl and strontium nitrates and uranyl chlorides in two room-temperature ionic liquids (ILs): [BMI][PF(6)] based on 1-butyl-3-methylimidazolium(+),PF(6)(-) and [EMI][TCA] based on 1-ethyl-3-methylimidazolium(+),AlCl(4)(-). Both dissociated M(2+),2NO(3)(-) and associated M(NO(3))(2) states of the salts are considered for the two cations, as well as the UO(2)Cl(2) and UO(2)Cl(4)(2)(-) uranyl complexes. In a [BMI][PF(6)] solution, the "naked" UO(2)(2+) and Sr(2+) ions are surrounded by 5.8 and 10.1 F atoms, respectively. The first-shell PF(6)(-) anions rotate markedly during the dynamics and are coordinated, on the average, monodentate to UO(2)(2+) and bidentate to Sr(2+). In an [EMI][TCA] solution, UO(2)(2+) and Sr(2+) coordinate 5.0 and 7.4 Cl atoms of AlCl(4)(-), respectively, which display more restricted motions. Four Cl atoms sit on a least motion pathway of transfer to uranyl, to form the UO(2)Cl(4)(2)(-) complex. The free NO(3)(-) anions and the UO(2)Cl(4)(2)(-) complex are surrounded by imidazolium(+) cations ( approximately 4 and 6-9, respectively). The first shell of the M(NO(3))(2) and UO(2)Cl(2) neutral complexes is mostly completed by the anionic components of the IL, with different contributions depending on the solvent, the M(2+) cation, and its counterions. Insights into energy components of solvation are given for the different systems.     

A molecular dynamics study of the interaction of oleate and dodecylammonium chloride surfactants with complex aluminosilicate minerals

Surface characteristics of complex aluminosilicate minerals like spodumene [LiAl(SiO(3))(2)], jadeite [NaAl(SiO(3))(2)], feldspar [KAlSi(3)O(8)], and muscovite [K(2)Al(4)(Al(2)Si(6)O(20))(OH)(4)]) are modeled. Surface energies are computed for the cleavage planes of these minerals. Adsorption mechanisms of anionic chemisorbing type oleate and cationic physisorbing type dodecylammonium chloride molecules on two different crystal planes, that is (110) and (001), of spodumene and jadeite are studied in terms of the surface-surfactant interaction energies computed using molecular dynamics (MD) simulations. The conclusions drawn from purely theoretical computations match remarkably well with our experimental results.