Molecular dynamics simulation of the equilibrium liquid–vapor interphase with solidification

The equilibrium structure of the finite, interphase interfacial region that exists between a liquid film and a bulk vapor is resolved by molecular dynamics simulation. Argon systems are considered for a temperature range that extends below the melting point. Physically consistent procedures are developed to define the boundaries between the interphase and the liquid and vapor phases. The procedures involve counting of neighboring molecules and comparing the results with boundary criteria that permit the boundaries to be precisely established. Two-dimensional radial distribution functions at the liquid and vapor boundaries and within the interphase region demonstrate the physical consistency of the boundary criteria and the state of transition within the region. The method developed for interphase boundary definitions can be extended to nonequilibrium systems. Spatial profiles of macroscopic properties across the interphase region are presented. A number of interfacial thermodynamic properties and profile curve-fit parameters are tabulated, including evaporation/condensation coefficients determined from molecular flux statistics. The evaporation/condensation coefficients away from the melting point compare more favorably with transition state theory than those of previous simulations. Near the melting point, transition theory approximations are less valid and the present results differ from the theory. The effects of film substrate wetting on evaporation/condensation coefficients are also presented.     

Why does β-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies

Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of other zymogens, is also partially active in cleaving APP. Hence, it is important to study on the mechanism of the zymogen's activation process. This study was to model the 3-D structure of the zymogen, followed by intensive molecular dynamics (MD) simulations to identify the most probable 3-D model and to study the dynamic structural behavior of the zymogen for understanding the effects of pro-segment on the function of the enzyme. The results revealed that the dropping in catalytic activity of the beta-secretase zymogen could be attributed to the occupation of the entrance of the catalytic site of the zymogen by its pro-segment. On the other hand, the partial catalytic activity of the zymogen could be explained by high fluctuation of the pro-segment in comparison with that of other zymogens, resulting in the occasionally exposure of the catalytic site for access its substrate APP. Indeed, steered MD (SMD) simulation revealed a weak pulling force at quasi-equilibrium state for the pro-segment of the zymogen leaving from the entrance, indicating that this swinging process could take place spontaneously. Furthermore, MM-PBSA calculation revealed a small change of free energy of 10.56 kal/mol between the initial and final states of the process of pro-segment swung outside the binding pocket of beta-secretase zymogen. These results not only account for the partial catalytic activity of beta-secretase zymogen, but also provide useful clues for discovering new potent ligands, as new type of drug leads for curing Alzheimer's disease, to prevent the pro-segment of the zymogen from leaving its catalytic site.     

Molecular dynamics simulation of surfactant effects on ion transport through a liquid–liquid interface between partially miscible liquids

Molecular dynamics (MD) simulations of water + 1-hexanol + NaCl mixtures with and without a surfactant (methanol) were performed to analyze the surfactant's effect on the transport of a sodium ion through the liquid–liquid interface. Without surfactant, the 1-hexanol forms a bilayer at the interface with OH groups directed outward toward the aqueous phase. Addition of the surfactant produces higher concentrations of the surfactant on the aqueous side of the interface without altering the organic bilayer structure. An electrical double-layer is created in both cases as chloride ion concentration is enhanced near the interface and sodium ion concentration is enhanced toward the center of the water phase. A potential of mean force (PMF) was calculated for the transfer of a sodium ion through the interface. Although the surfactant reduced the interfacial tension, the total work required for the ion transfer increased with the addition of the surfactant.     

Hydrogen atom loss from the benzene cation. Why is the kinetic energy release so large?

The kinetic energy release distributions (KERDs) associated with the hydrogen loss from the benzene cation and the deuterium loss from the perdeuteriobenzene cation have been remeasured on the metastable time scale and analyzed by the maximum entropy method. The experimental kinetic energy releases are larger than expected statistically, in contradistinction to what has been observed for the C-X fragmentations of the halogenobenzene cations. H(D) loss from C(6)H(6)(+) (C(6)D(6)(+)) occurs via a conical intersection connecting the (2)A(2) and (2)A(1) electronic states. Two models are proposed to account for the experimental data: (i) a modified orbiting transition state theory (OTST) approach incorporating electronic nonadiabaticity; (ii) an electronically nonadiabatic version of the statistical adiabatic channel model (SACM) of Quack and Troe. The latter approach is found to be preferable. It leads to the conclusion that the larger the energy stored in the transitional modes, which partly convert to the relative interfragment motion, the shorter the value of the reaction coordinate at which the adiabatic channels cross, and the larger the probability of undergoing the (2)A(2) --> (2)A(1) transition required for hydrogen loss.     

Molecular dynamics simulation on explosive boiling of thin liquid argon films on cone-shaped Al–Cu-based nanostructures

Journal of Thermal Analysis and Calorimetry - The aim of this study is to investigate the effects of Al and Cu nanostructures on the explosive boiling of a thin layer of liquid argon atoms on the...     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

Molecular simulation of the phase behaviour of ternary fluid mixtures: the effect of a third component on vapour–liquid and liquid–liquid coexistence

The Gibbs ensemble algorithm is implemented to determine the vapour–liquid and liquid–liquid phase coexistence of dilute ternary fluid mixtures interacting via a Lennard–Jones potential. Calculations are reported for mixtures with a third component characterised by different intermolecular potential energy parameters. Comparison with binary mixture data indicates that the choice of energy parameter for the third component affects the composition range of vapour–liquid substantially. The addition of a third component lowers the energy of liquid phase while slightly increasing the energy of the vapour phase.     

Molecular dynamics simulation studies of the ε-CL-20/HMX co-crystal-based PBXs with HTPB

Molecular dynamics simulations were carried out to explore a ε-CL-20/HMX (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexazaisowurtzitane/1,3,5,7-tetranitro-1,3,5,7- tetrazacyclooctane) co-crystal-based polymer-bonded explosive (PBX) with HTPB (hydroxyl-terminated polybutadiene). The binding energies, pair correlation functions, and mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that the order of the binding energies per unit surface between the crystalline surface and HTPB is (0 1 0) > (1 0 0) > (0 0 1). The pair correlation function revealed that the H···O and H···N H-bonds exist on the interfaces between the crystalline surfaces and HTPB, and the number of H???O hydrogen bonds (H-bonds) atom pairs is ten times more than that of H???N H-bonds. Additionally, the calculated mechanical data indicated that the stiffness of the co-crystal/HTPB PBX is weaker and its ductility is better than those of the co-crystal.     

Molecular dynamics simulation of local motion of polystyrene chain end—comparison with the fluorescence depolarization study

Molecular dynamics (MD) simulation of the local motion of a polystyrene (PS) chain with anthryl group at the chain end surrounded by benzene molecules was performed and the results were compared with those obtained experimentally by the fluorescence depolarization method. The molecular weight dependence of the relaxation time of the probe obtained by the MD simulation was qualitatively in agreement with the results obtained by the fluorescence depolarization method. We also estimated the molecular weight dependence of the relaxation time for the end-to-end vector. Below the degree of polymerization (DP)≤3, the mean relaxation time T_m for the end-to-end vector was similar to that for the vector corresponding to the transition moment of the probe. With the increase of DP, the T_m for the probe tended to reach an asymptotic value unlike that for the end-to-end vector, which monotonically increased with DP. This indicates that the entire motion of a polymer coil contributes to the local motion to a lesser extent as the molecular weight increases. The MD simulations using artificial restraints showed that the rotational relaxation of the probe at the chain end for a dynamically stiff PS chain is realized by the cooperative rotation of the main chain bonds. The internal modes which takes place below 5 monomer units mainly led to the rotational relaxation of the probe at the PS chain end. Finally, the change of T_m with the position along the PS main chain was examined.     

Molecular dynamics simulation of liquid CH2Cl2 with 3×3 and 5×5 site-site interactions

A molecular dynamics simulation of liquid CH₂Cl₂ is compared with the far infrared spectrum at the same state point (293K, 1 bar). Two representations of the force field are used, a 3×3 and 5×5 site-site interaction consisting of Lennard-Jones and charge terms. The far infra-red spectrum shows unambiguously that the 5×5 representation is more realistic in the sense that it reproduces the observed spectrum more closely.     

Why does silane enhance the protective properties of epoxy films?

Using neutron reflectivity, the protection mechanisms of a novel one-step epoxy-silane coating system were investigated in terms of coating structure and water response behavior. By comparing pure epoxy and epoxy-silane mixtures in various aqueous environments, the effects of the addition of silane were determined. Specifically, a bridged bis-silane coupling agent with six alkoxy moieties and a polysulfur bridge was investigated. The key mechanisms of silane-enhanced protection are (1) the silane is enriched at the substrate-coating interface, forming a hydrophobic dense interfacial layer and good adhesion to the substrate, and (2) the silane serves as a cross-linker, resulting in a denser and less hydrophilic bulk film compared to the neat epoxy. The hydrophobic nature of bis-sulfur silane also increases the overall hydrophobicity of the mixed film.     

Why does cyclopropene have the acidity of an acetylene but the bond energy of methane?

The gas-phase acidity of 3,3-dimethylcyclopropene (1) has been measured by bracketing and equilibrium techniques. Consistent with simple hybridization arguments, our value (deltaH degrees (acid) = 382.7 +/- 1.3 kcal mol(-)(1)) is indistinguishable from that for methylacetylene (i.e., deltadeltaH degrees (acid)(1 - CH(3)Ctbd1;CH) = 1.6 +/- 2.5 kcal mol(-)(1)). The electron affinity of 3,3-dimethylcyclopropenyl radical (1r) was also determined (EA = 37.6 +/- 3.5 kcal mol(-)(1)), and these quantities were combined in a thermodynamic cycle to afford the homolytic C-H bond dissociation energy. To our surprise, the latter quantity (107 +/- 4 kcal mol(-)(1)) is the same as that for methane, which cannot be explained in terms of the s-character in the C-H bonds. An orbital explanation (delocalization) is proposed to account for the extra stability of 1r. All of the results are supplemented with G3 and B3LYP computations, and both approaches are in good accord with the experimental values. We also note that for simple hydrocarbons which give localized carbanions upon deprotonation there is an apparent linear correlation between any two of the following three quantities: deltaH degrees (acid), BDE, and EA. This observation could be of considerable value in many diverse areas of chemistry.     

Molecular dynamics simulation of the key characteristics of the supercritical CO<Subscript>2</Subscript>–pentaerythritol tetraacetate system

Supercritical CO₂ is widely used in many fields of industry. Investigation of statistical mechanics of CO₂ fluid under quasi critical and supercritical state has great significance. Equilibrium molecular dynamics (EMD) simulations are carried out to investigate the statistical mechanics and macroscopic performance of CO₂ fluid under the quasi critical and supercritical state. The results show that the bond length and bond angle distributions for supercritical CO₂ are Gaussian distribution basically. The dimers’ proportion of supercritical CO₂ system changes with pressure increasing. T-type dimer has high share within the system when pressure is higher than 9MPa. It can be inferred that T-type dimer leads to CO₂ physical properties changing tempestuously under supercritical state. The effect that lubricating oil has on microstructure and heat transfer of supercritical CO₂ is also investigated in the present work. The results show the lubricating oil produces significant effect on the dimers’ structure under low pressure.     

How does water affect the dynamics of the room-temperature ionic liquid 1-hexyl-3-methylimidazolium hexafluorophosphate and the fluorescence spectroscopy of Coumarin-153 when dissolved in it?

Molecular dynamics simulations of mixtures of 1-hexyl-3-methylimidazolium hexafluorophosphate ([HMIM+][PF6-]) and water have been performed in order to investigate how small amounts of water affect the translational and rotational dynamics of this ionic liquid (IL). We find that water is closely associated with the anions and that its presence enhances both the translational and rotational dynamics of the IL. In agreement with experiments, we find that the fluorescence spectra of Coumarin-153 is red-shifted because of the presence of water. Small amounts of water enhance the speed of relaxation of the solvent surrounding the solute probe after photoexcitation, but only at a "local environment" level. Interconversion between environments still occurs on a long time scale compared with the fluorescence lifetime of the probe. Excitation wavelength-dependent emission is observed both in the neat IL and in the IL+water mixture.     

Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with p38α MAP kinase

p38 MAP kinase is a promising target for anti-inflammatory treatment. The classical kinase inhibitors imatinib and sorafenib as well as BI-1 and BIRB-796 were reported to bind in the DFG-out form of human p38α, known as type II or allosteric kinase inhibitors. Although DFG-out conformation has attracted great interest in the design of type II kinase inhibitors, the structural requirements for binding and mechanism of stabilization of DFG-out conformation remain unclear. As allosteric inhibition is important to the selectivity of kinase inhibitor, herein the binding modes of imatinib, sorafenib, BI-1 and BIRB-796 to p38α were investigated by molecular dynamics simulation. Binding free energies were calculated by molecular mechanics/Poisson-Boltzmann surface area method. The predicted binding affinities can give a good explanation of the activity difference of the studied inhibitors. Furthermore, binding free energies decomposition analysis and further structural analysis indicate that the dominating effect of van der Waals interaction drives the binding process, and key residues, such as Lys53, Gly71, Leu75, Ile84, Thr106, Met109, Leu167, Asp168, and Phe169, play important roles by forming hydrogen bond, salt bridge, and hydrophobic interactions with the DFG-out conformation of p38α. Finally, we also conducted a detailed analysis of BI-1, imatinib, and sorafenib binding to p38α in comparison with BIRB-796 exploited for gaining potency as well as selectivity of p38 inhibitors. These results are expected to be useful for future rational design of novel type II p38 inhibitors.     

How does ammonium dynamically interact with benzene in aqueous media? A first principle study using the Car-Parrinello molecular dynamics method

The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between ammonium and benzene is stable even in aqueous solution. Thus, this CPMD study suggested that the cation-pi interaction between an ammonium (group) and an aromatic structure could take place even on surfaces of protein or nucleic acids in solution.     

Why intermolecular nitric oxide (NO) transfer? Exploring the factors and mechanistic aspects of NO transfer reaction

Small molecule activation and their transfer reactions in biological or catalytic reactions are greatly influenced by the metal-centers and the ligand frameworks. Here, we report the metal-directed nitric oxide (NO) transfer chemistry in low-spin mononuclear {Co(NO)}⁸, [(12-TMC)Co^III(NO⁻)]²⁺ (1-CoNO, S = 0), and {Cr(NO)}⁵, ([(BPMEN)Cr(NO)(Cl)]⁺) (4-CrNO, S = 1/2) complexes. 1-CoNO transfers its bound NO moiety to a high-spin [(BPMEN)Cr^II(Cl₂)] (2-Cr, S = 2) and generates 4-CrNOvia an associative pathway; however, we did not observe the reverse reaction, i.e., NO transfer from 4-CrNO to low-spin [(12-TMC)Co^II]²⁺ (3-Co, S = 1/2). Spectral titration for NO transfer reaction between 1-CoNO and 2-Cr confirmed 1 : 1 reaction stoichiometry. The NO transfer rate was found to be independent of 2-Cr, suggesting the presence of an intermediate species, which was further supported experimentally and theoretically. The experimental and theoretical observations support the formation of μ-NO bridged intermediate species ({Cr–NO–Co}⁴⁺). Mechanistic investigations using ¹⁵N-labeled-¹⁵NO and tracking the ¹⁵N-atom established that the NO moiety in 4-CrNO is derived from 1-CoNO. Further, to investigate the factors deciding the NO transfer reactivity, we explored the NO transfer reaction between another high-spin Cr^II-complex, [(12-TMC)Cr^II(Cl)]⁺ (5-Cr, S = 2), and 1-CoNO, showing the generation of the low-spin [(12-TMC)Cr(NO)(Cl)]⁺ (6-CrNO, S = 1/2); however, again there was no opposite reaction, i.e., from Cr-center to Co-center. The above results advocate clearly that the NO transfer from Co-center generates thermally stable and low-spin and inert {Cr(NO)}⁵ complexes (4-CrNO & 6-CrNO) from high-spin and labile Cr-complexes (2-Cr & 5-Cr), suggesting a metal-directed NO transfer (cobalt to chromium, not chromium to cobalt). These results explicitly highlight that the NO transfer is strongly influenced by the labile/inert behavior of the metal-centers and/or thermal stability rather than the ligand architecture.

Nitric oxide activation and parameters influencing intermolecular transfer of nitric oxide.     

Why is the partial molar volume of CO2 so small when dissolved in a room temperature ionic liquid? Structure and dynamics of CO2 dissolved in [Bmim+] [PF6(-)

When supercritical CO2 is dissolved in an ionic liquid, its partial molar volume is much smaller than that observed in most other solvents. In this article we explore in atomistic detail and explain in an intuitive way the peculiar volumetric behavior experimentally observed when supercritical CO2 is dissolved in 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim+] [PF6(-)]). We also provide physical insight into the structure and dynamics occurring across the boundary of the CO2 ionic liquid interface. We find that the liquid structure of [Bmim+] [PF6(-)] in the presence of CO2 is nearly identical to that in the neat ionic liquid (IL) even at fairly large mole fractions of CO2. Our simulations indicate, in agreement with experiments, that partial miscibilities of one fluid into the other are very unsymmetrical, CO2 being highly soluble in the ionic liquid phase while the ionic liquid is highly insoluble in the CO2 phase. We interpret our results in terms of the size and shape of spontaneously forming cavities in the ionic liquid phase, and we propose that CO2 occupies extremely well-defined locations in the IL. Even though our accurate prediction of cavity sizes in the neat IL indicates that these cavities are small compared with the van der Waals radius of a single carbon or oxygen atom, CO2 appears to occupy a space that was for the most part a priori "empty".     

Optical pump-terahertz probe spectroscopy of dyes in solutions: probing the dynamics of liquid solvent or solid precipitate?

The optical pump-terahertz probe spectroscopy was used together with ab initio calculations and molecular dynamics simulations to investigate ultrafast dynamics following electronic excitation of Coumarin 153 and TBNC (2,11,20,29-tetra-tert-butyl-2,3-naphtalocyanine) dyes in polar solvents. By scanning the terahertz waveform for different pump-probe delays this experimental technique allows us to obtain two dimensional spectra directly reflecting the temporal response of the system. A distinct signal was obtained for TBNC in chloroform, 2-propanol, and n-butanol, while no signal was recorded for Coumarin 153 in either of these solvents. We explain the nonequilibrium signal detected in TBNC solutions by the presence of a solid, polycrystalline phase of the dye resulting from irradiating the solution by intense optical pulses.     

How short can the H...H intermolecular contact be? New findings that reveal the covalent nature of extremely strong interactions

Ab initio calculations at the MP2/6-311++G(d,p) and MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ levels have been performed for the following complexes: H2OH+...HBeH, H2OH+...HBeBeH, H2OH+...HBeF, HClOH+...HBeH, Cl2OH+...HBeH, and Cl2OH+...HBeF. For all dimers considered, extremely short H...H intermolecular contacts (1.0-1.3 A) were obtained. These are the shortest intermolecular distances which have ever been reported, with binding energies within the range of 13.7-24.3 kcal/mol (MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ level). The interaction energies of the complexes analyzed were also extrapolated to the complete basis set (CBS) limit. To explain the nature of such strong interactions, the Bader theory was applied, and the characteristics of the bond critical points (BCPs) were analyzed. It was pointed out that for the major part of the H...H contacts considered here the Laplacian of the electron density at H...H BCP is negative indicating the partly covalent nature of such a connection. The term "covalent character of the hydrogen bond" used sometimes in recent studies is discussed. An analysis of the interaction energy components for dihydrogen bonded systems considered indicates that in contrast to conventional hydrogen bonded systems the attractive electrostatic term is outweighed by the repulsive exchange energy term and that the higher order delocalization energy term is the most important attractive term.