Molecular dynamics simulations on the structures and properties of ε-CL-20-based PBXs ——Primary theoretical studies on HEDM formulation design

Five polymer bonded explosives (PBXs) with the base explosive ε-CL-20 (hexanitrohexaazaisowurtzi- tane), the most important high energy density compound (HEDC), and five polymer binders (Estane 5703, GAP, HTPB, PEG, and F2314) were constructed. Molecular dynamics (MD) method was employed to investigate their binding energies (Ebind), compatibility, safety, mechanical properties, and energetic properties. The information and rules were reported for choosing better binders and guiding formula- tion design of high energy density material (HEDM). According to the calculated binding energies, the ordering of compatibility and stability of the five PBXs was predicted as ε-CL-20/PEG > ε-CL-20/ Estane5703 ≈ε-CL-20/GAP > ε-CL-20/HTPB > ε-CL-20/F2314. By pair correlation function g(r) analyses, hydrogen bonds and vdw are found to be the main interactions between the two components. The elasticity and isotropy of PBXs based ε-CL-20 can be obviously improved more than pure ε-CL-20 crystal. It is not by changing the molecular structures of ε-CL-20 for each binder to affect the sensitivity. The safety and energetic properties of these PBXs are mainly influenced by the thermal capability (C°p) and density (ρ) of binders, respectively.     

Molecular dynamics simulations on the structures and properties of ε-CL-20-based PBXs——Primary theoretical studies on HEDM formulation design

Five polymer bonded explosives (PBXs) with the base explosiveε-CL-20 (hexanitrohexaazaisowurtzitane), the most important high energy density compound (HEDC), and five polymer binders (Estane 5703, GAP, HTPB, PEG, and F2314) were constructed. Molecular dynamics (MD) method was employed to investigate their binding energies (Ebind), compatibility, safety, mechanical properties, and energetic properties. The information and rules were reported for choosing better binders and guiding formulation design of high energy density material (HEDM). According to the calculated binding energies, the ordering of compatibility and stability of the five PBXs was predicted as ε-CL-20/PEG ＞ ε-CL-20/ Estane5703 ≈ε-CL-20/GAP ＞ ε-CL-20/HTPB ＞ ε-CL-20/F2314. By pair correlation function g(r) analyses, hydrogen bonds and vdw are found to be the main interactions between the two components. The elasticity and isotropy of PBXs based ε-CL-20 can be obviously improved more than pure ε-CL-20 crystal. It is not by changing the molecular structures of ε-CL-20 for each binder to affect the sensitivity. The safety and energetic properties of these PBXs are mainly influenced by the thermal capability (C°p) and density (ρ) of binders, respectively.     

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.     

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.     

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.     

Effect of addictives on polymorphic transition of ε-CL-20 in castable systems

In order to explore the law of polymorphic transformation in the process of preparing hexanitrohexaazaisowurtzitane (CL-20)-based composite explosives in cast-cured method, the polymorphic transition of CL-20 crystal under heat stimulation was investigated by X-ray diffraction and differential scanning calorimetric method, respectively, and the effects of different addictives (mainly involved in castable systems) on polymorphic transition of CL-20 were elaborately explored. The transition mechanism was systemically analyzed from the point of view of kinetic and thermodynamic. The experiment results showed that the polymorphic transition was closely related to temperature and ambient surroundings, and the influence of different additives was not consistent in the process of polymorphic transition. In addictives with higher dipole moment or solubility of CL-20, ε-form could easily be polarized and tend to transform into γ-form and the process occurred in fluid medium was much easier than that in solid matrix. The investigation contributes to comprehend the polymorphic transformation mechanism of CL-20 and provides guidance for effective control on the CL-20 polymorphs in preparing CL-20-based composite explosives.     

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".     

Why does the intermolecular dynamics of liquid biphenyl so closely resemble that of liquid benzene? Molecular dynamics simulation of the optical-Kerr-effect spectra

The combination of optical-Kerr-effect (OKE) spectroscopy and molecular dynamics simulations has provided us with a newfound ability to delve into the librational dynamics of liquids, revealing, in the process, some surprising commonalities among aromatic liquids. Benzene and biphenyl, for example, have remarkably similar OKE spectra despite marked differences in their shapes, sizes, and moments of inertia--and even more chemically distinct aromatics tend to have noticeable similarities in their spectra. We explore this universality by using a molecular dynamics simulation to investigate the librational dynamics of molten biphenyl and to predict its OKE spectrum, comparing the results with our previous calculations for liquid benzene. We suggest that the impressive level of quantitative agreement between these two liquids is largely a reflection of the fact that librations in these and other aromatic liquids act as torsional oscillations with oscillator frequencies selected from the liquid's librational bands. Since these bands are centered about the librational Einstein frequencies, the quantitative similarities between the liquids are essentially reflections of the near identities of their Einstein frequencies. Why then are the Einstein frequencies themselves so insensitive to molecular details? We show that, for nearly planar molecules, mean-square torques and moments of inertia tend to scale with molecular dimensions in much the same way. We demonstrate that this near cancellation provides both a quantitative explanation of the close relationship between benzene and biphenyl and a more general perspective on the similarities seen in the ultrafast dynamics of aromatic liquids.     

Molecular dynamics studies of α-helix stability in fibril-forming peptides

Diseases associated with protein fibril-formation, such as the prion diseases and Alzheimer’s disease, are gaining increased attention due to their medical importance and complex origins. Using molecular dynamics (MD) simulations in an aqueous environment, we have studied the stability of the α-helix covering positions 15–25 of the amyloid β-peptide (Aβ) involved in Alzheimer’s disease. The effects of residue replacements, including the effects of Aβ disease related mutations, were also investigated. The MD simulations show a very early (2 ns) loss of α-helical structure for the Flemish (Aβ(A21G)), Italian (Aβ(E22K)), and Iowa (Aβ(D23N)) forms associated with hereditary Alzheimer’s disease. Similarly, an early (5 ns) loss of α-helical structure was observed for the Dutch (Aβ(E22Q)) variant. MD here provides a possible explanation for the structural changes. Two variants of Aβ, Aβ(K16A,L17A,F20A) and Aβ(V18A,F19A,F20A), that do not produce fibrils in vitro were also investigated. The Aβ(V18A,F19A,F20A) initially loses its helical conformation but refolds into helix several times and spends most of the simulation time in helical conformation. However, the Aβ(K16A,L17A,F20A) loses the α-helical structure after 5 ns and does not refold. For the wildtype Aβ(1–40) and Aβ(1–42), the helical conformation is lost after 5 ns or after 40 ns, respectively, while for the “familial” (Aβ(A42T)) variant, the MD simulations suggest that a C-terminal β-strand is stabilised, which could explain the fibrillation. The simulations for the Arctic (Aβ(E22G)) variant indicate that the α-helix is kept for 2 ns, but reappears 2 ns later, whereafter it disappears after 10 ns. The MD results are in several cases compatible with known experimental data, but the correlation is not perfect, indicating that multimerisation tendency and other factors might also be important for fibril formation.     

Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies

Garcinia kola (GK) produces notable effects against neurodegenerative conditions, including experimentally-induced Alzheimer’s disease (AD). These remarkable effects are basically attributable to kolaviron (KV), a bioflavonoid constituent of this seed. Specifically, it has been reported that in AD models, KV produces interesting neuroprotective effects, being able to diminish associated neurotoxicity, via modulation of antioxidative, inflammatory and other disease modifying processes. Intriguingly, the effect of KV on amyloid-beta (Aβ) aggregation and disruption of preformed Aβ fibrils have not been studied. In this study, we have described a thorough computational study on the mechanism of action of KV as an Aβ fibrils disruptor at molecular level. We used comprehensive in silico docking evaluations and extended molecular dynamics simulation to mimic KV/Aβ fibrils system. Results indicate that KV was able to move within the Aβ fibrils, binding with important residues and components in the Aβ peptide identified to be vital for stabilizing preformed fibrils. KV destabilized the assembled Aβ fibrils, indicating the ability KV as a potential anti-amyloidogenic agent. Furthermore, this work highlighted the possibility of identifying new multifunctional phytocompounds as potent AD drugs.     

Molecular dynamics studies of the inhibitory mechanism of copper（Ⅱ） on aggregation of amyloid β-peptide

The inhibitory mechanism of copper（Ⅱ） on the aggegation of amyloid β-peptide （Aβ） was investigated by molecular dynamics simulations. The binding mode ofcopper（Ⅱ） with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H 13, acting as the anchoring site, and the backbone＇s deprotoned amide nitogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.     

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.     

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

Biguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.     

Molecular dynamics simulation in aqueous solution of N-methylazetidinone as a model of β-lactam antibiotics

In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the first type, the β-lactam-water interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the β-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent effect is included. Received: 29 July 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999     

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.     

Molecular simulation of the Joule–Thomson inversion curve of carbon dioxide

The complete Joule–Thomson (JT) inversion curve for carbon dioxide is calculated using molecular simulations. A two center Lennard–Jones model with an embedded point quadrupole is used to model the fluid–fluid interactions. The simulation results agree quantitatively with all available experimental data. Comparison with commonly used equations of state provides only a modest agreement, with the highest discrepancies being observed at the high temperature branch of the inversion curve.     

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.     

Molecular dynamics of ��-CD in water/co-solvent mixtures

Molecular dynamics (MD) simulations on ??-cyclodextrin (??-CD) in water, ethanol (EtOH), methanol (MeOH) and mixtures of these solvents have been carried out at 300 K over a time period of 15 ns using the AMBER force field. The hydrated X-ray crystallographic structure has four water molecules inside the cavity, defined by a more precise boundary for the ??-CD cavity. From the simulations, 2?C4 encapsulated water molecules are most probably found. In an ethanol co-solvent system, the ??-CD cavity is occupied with one ethanol molecule located in two discrete sites: below and above the O4(n) plane, which is in agreement with experimental results. In all systems, the average values of tilt angles of the obtained structures are higher than the tilt angles of the X-ray structures. The investigations of the alcohol orientations in co-solvent mixtures reveal the hydrophobic environment of the cavity and the hydrophilic atmosphere at both rims of ??-CD.     

Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex

A complete understanding of gene expression relies on a comprehensive understanding of the protein-RNA recognition process. However, the study of protein-RNA recognition is complicated by many factors that contribute to both binding affinity and specificity, including structure, energetics, dynamical motions, and cooperative interactions. Several recent studies have suggested that energetic coupling between residues contributes to formation of the complex between the U1A protein and stem loop 2 of U1 snRNA as a consequence of a cooperative network of interactions. We have performed molecular dynamics simulations on the U1A-RNA complex, including explicit water and counterions, and analyzed the results based on the calculated positional cross-correlations of atomic fluctuations. The results indicate that cross-correlations calculated on a per residue basis agree well with the observed inter-residue cooperativity and predict that the networks identified to date may also be coupled into an extensive hyper-network that reflects the intrinsic rigidity of the RNA recognition motif. In addition, we report a comparison of the MD calculated correlations with the results of a positional covariance analysis based on the sequences of 330 RNA recognition motifs, including U1A. The calculated inter-residue cross-correlations agree very well with the results of the sites exhibiting positional covariance. Collectively, these results strongly support the hypothesis that collective fluctuations contribute to cooperativity and the corresponding observed thermodynamic coupling. Predictions of additional sites in U1A that may be involved in cooperative networks are advanced.