Molecular dynamics and quantum chemical studies on nitroglycerine

A constant temperature molecular dynamics study has been performed on PM3 (RHF) geometry optimized nitroglycerine molecule. The dynamics was carried out by using MM+ method at 550 K which is above the explosion point of nitroglycerine. Some molecular orbital characteristics of nitroglycerine at elevated temperatures were computed.     

Molecular orientation of monododecyl pentaethylene glycol at water/air and water/oil interfaces. A molecular dynamics computer simulation study

With a molecular dynamics computer simulation we investigated the dynamic properties of a monododecyl pentaethylene glycol (C₁₂E₅) molecule adsorbed at air/water and oil/water interfaces. In these simulations we investigated the molecular orientation of the surfactant molecules in detail. At the air/water interface the maximum of the C₁₂ chain tilt angle distribution measured with respect to the water surface is about 50°. This result is in fairly good agreement with neutron reflection experiments of monododecyl glycol ethers at the air/water interface. At the oil/water interface no significant changes were detected in the molecular orientation. We found that at equilibrium oil molecules penetrate into the hydrophobic monododecyl layer, this was also found by neutron reflection studies of the interactions between C₁₂E₅ and dodecane. The observed oil penetration results in an increase in the surface area per surfactant molecule. Received: 16 July 1999/Accepted in revised form: 28 August 1999     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

表面活性剂界面自组装的分子动力学模拟

主要介绍了表面活性剂在液／液、气／液和固／液界面的自组装,详细讨论了分子动力学模拟在表面活性剂界面自组装体系的应用,指出了近年来该领域的发展现状及应用前景。     

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 ...     

Molecular recognition of sulfonatocalixarene with organic cations at the self-assembled interface: a thermodynamic investigation

A microcalorimetric study on molecular recognition of p-sulfonatocalix[4]arene derivatives at selfassembled interface in comparison with in bulk water was performed,inspired by the dramatic change in physicochemical characteristics from bulk water to interface.A total of six cationic molecules were screened as model guests,including ammonium(NH_4~+),guanidinium(Gdm~+).N,N'-dimethyl-1,4-diazabicyclo[2.2.2]octane(DMDABCO~(2+)),tropylium(Tpm~+),N-methyl pyridinium(N-mPY*) and methyl viologen(MV~(2+)).The complexation with NH_4~+.Gdm~+ and DMDABCO2* is pronouncedly enhanced when the recognition process moved from bulk water to interface,whereas the complexation stabilities with Tpm~+,N-mPY~+ and MV2* increase slightly or even decrease to some extent.A more interesting phenomenon arises from the NH_4~+/Gdm~+ pair that the thermodynamic origin at interface differs definitely from each other although with similar association constants.The results were discussed in terms of differential driving forces,electrostatic,hydrogen bond as well as π-stacking interactions,originating from the unique physicochemical features of interfaces,mainly the polarity and dielectric constant.     

Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH

Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues – ASN14, THR18 and GLN44 – involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications.     

Spectroscopic studies on bilirubin aggregate at liquid/liquid interface

Bilirubin (BR) aggregating at liquid/liquid interface was firstly detected by Fourier transform infrared (FTIR) imaging/spectroscopy combining with ultraviolet-visible (UV/Vis) absorption spectra. In the UV/Vis absorption spectra of BR aggregate, a new shoulder appeared at 474 nm, and BR absorption maximum underwent red shift from 450 nm to a longer wavelength at 497 nm, which indicates that BR aggregate was formed at the interface. Meanwhile, the BR molecule structure changed or conformation torsion, that is, the increase in orbit overlap or dihedral angle and the enhancement of exciton coupling. In the study of FTIR imaging/spectroscopy, the hydrogen bond-sensitive infrared bands of BR aggregate showed remarkable changes in band shift and intensity compared with those of BR powder, suggesting that the intramolecular hydrogen bonds broke out and internal structure changed. These new findings will be helpful for understanding of the BR molecular interaction, transportation, complex with serum albumin and metal ions, and the effect of BR aggregating on biomembrane and human tissues.

Molecular dynamics simulations of amphiphilic graft copolymer molecules at a water/air interface

Fully atomistic molecular dynamics simulations of amphiphilic graft copolymer molecules have been performed at a range of surface concentrations at a water/air interface. These simulations are compared to experimental results from a corresponding system over a similar range of surface concentrations. Neutron reflectivity data calculated from the simulation trajectories agrees well with experimentally acquired profiles. In particular, excellent agreement in neutron reflectivity is found for lower surface concentration simulations. A simulation of a poly(ethylene oxide) (PEO) chain in aqueous solution has also been performed. This simulation allows the conformational behavior of the free PEO chain and those tethered to the interface in the previous simulations to be compared.     

Topography of bent-core liquid crystals at the air/liquid crystal interface

Bent-core liquid crystals show a variety of novel structures involving the interplay of molecular bend, tilt and polarisation. Here we investigate the microstructures of the B4, B7 and the dark conglomerate (DC) phases at the air/liquid crystal interface. In these phases, bent-core molecules undergo complex self-assembly, forming helical nanofilaments (the B4 phase), layer undulations (the B7 phase) and disordered focal conics (the DC phase) in the bulk. However, due to the fluidity of the phases and the homeotropic alignment at the interface, several different topographies are observed at the air/liquid crystal interface. We will discuss the surface structures discovered so far in the B4, B7 and DC phases and show how they help us to understand the microstructure and the self-assembly of the liquid crystal phases of bent-core molecules.     

Adsorption of sodium octylbenzene-sulfonate at the liquid/air interface

The surface tensions of aqueous solutions containing sodium octylbenzenesulfonate were measured by means of a processor tensiometer at 20°, 25°, 30° and 35°C. A test for the layer model and thickness of the adsorbed phase is proposed. By means of a linear regression the surfactant area at liquid/air interface was calculated. Finally, the molar-and surface-related thermodynamic functions were discussed.     

Molecular dynamics on distributed memory (MIMD) parallel computers

Summary Several algorithms are described that have been applied to molecular dynamics simulations and their merits discussed. The subject matter is confined to distributed (MIMD) algorithms. A simple mathematical model is used to illustrate the performance characteristics of a parallel MD algorithm.     

Solute rotational dynamics at the water liquid/vapor interface

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Salt effect on molecular orientation at air/liquid methanol interface

The salt effects on molecular orientation at air/liquid methanol interface were investigated by the polarization-dependent sum frequency generation vibrational spectroscopy(SFG-VS). We clarified that the average tilting angle of the methyl group to be u = 308 58 at the air/pure methanol surface assuming a d-function orientational distribution. Upon the addition of 3 mol/L Na I, the methyl group tilts further away from the surface normal with a new u = 418 38. This orientational change does not explain the enhancement of the SFG-VS intensities when adding Na I, implying the number density of the methanol molecules with a net polar ordering in the surface region also changed with the Na I concentrations. These spectroscopic findings shed new light on the salt effects on the surfaces structures of the polar organic solutions. It was also shown that the accurate determination of the bulk refractive indices and Raman depolarization ratios for different salt concentrations is crucial to quantitatively interpret the SFG-VS data.     

Compression studies on a monolayer of polymer stabilized latices at the air/2 molar sodium chloride solution interface

Summary The two dimensional compression technique ofDoroszkowski et al. has been used to study the steric repulsion force for a monolayer of poly(vinyl pyrrolidone) stabilized polystyrene latex particles spread at the Air/2M sodium chloride solution interface. Repulsion forces were first detected at a particle separation of 150 nm with a dramatic increase in repulsion at about 15 nm.

---

Zusammenfassung Die sterische Abstoßung zwischen Polystyrol-Latexteilchen in einer Monoschicht wurde nach der Methode vonDoroszkowski et al. gemessen. Die Latexteilchen waren mit Polyvinylpyrrolidon stabilisiert und an der Grenzfläche einer 2M Natriumchloridlösung zur Luft gespreitet. Die Abstoßungskräfte machten sich bei einer Annäherung der Teilchen auf 150 nm zum 1. Mal bemerkbar. Sie stiegen drastisch an bei etwa 15 nm.

---

---

With 4 figures and 1 table     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Phase behavior of amphiphiles at liquid crystals/water interface: A coarse-grained molecular dynamics study

We present a coarse-grained molecular dynamics simulation study of phase behavior of amphiphilic monolayers at the liquid crystal （LC）/water interface. The results revealed that LCs at interface can influence the lateral ordering of amphiphiles. Particularly, the amphiphile tails along with perpendicularly penetrated LCs between tails undergo a two-dimension phase transition from liquid-expanded into a liquid-condensed phase as their area density at interface reaches 0.93. While, the liquid-condensed phase of the monolayer never appears at oil/water interface with isotropic shape oil particles. These findings reveal the penetration of anisotropic LC can promote ordered lateral organization of amphiphiles. Moreover, we find the phase transition point is shifted to lower surface coverage of amphiphiles when the LCs have larger affinity to the amphiphile tails.     

Impact of an ionic surfactant on the ion transfer behaviors at meso-liquid/liquid interface arrays

The influence of ionic surfactants,cetyltrimethylammonium bromide(CTAB),self-assembled within silica-nanochannels of a hybrid mesoporous silica membrane(HMSM) on simple ion transfer(IT)behaviors at the meso-water/1,2-dichloroethane(W/DCE) interface arrays supported by such a HMSM was investigated by voltammetry for the first time.Significantly,it is found that the CTAB in HMSM can dramatically enhance the peak-current responses corresponding to ITs of some anions and even lower their Gibbs transfer energies from W to DCE,which could be ascribed to an anion-exchange process between anions and the bromide of CTAB associated with partial ion-dehydration induced by the CTAB.This work will provide a new strategy to study anion transfer processes and improve the electroanalytical performance for anion detection at the liquid/liquid interface.     

Discotic liquid crystals at the air water interface

The monolayer properties of two types of discotic liquid crystals, hexasubstituted triphenylenes 1 and azo derivatives of phloroglucinol 5, were examined. First investigations show that these discotic liquid crystals form stable monolayers. It could be shown that electron acceptors insert into the monolayer of 1. Azo discs display a packing behaviour at the monolayer that is ascribed to a side-on packing of the molecules.