Theoretical insights into the effects of molar ratios on stabilities,mechanical properties,and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation

To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.     

Molecular dynamics calculation on structures,stabilities, mechanical properties,and energy density of CL-20/FOX-7 cocrystal explosives

In this article, different CL-20/FOX-7 cocrystal models were established by the substitution method based on the molar ratios of CL-20:FOX-7. The structures and comprehensive properties, including mechanical properties, stabilities, and energy density, of different cocrystal models were obtained and compared with each other. The main aim was to estimate the influence of molar ratios on properties of cocrystal explosives. The molecular dynamics (MD) simulation results show that the cocrystal model with molar ratio 1:1 has the best mechanical properties and highest binding energy, so the CL-20/FOX-7 cocrystal model is more likely to form in 1:1 M ratio. The detonation parameters show that the cocrystal explosive exhibited preferable energy density and excellent detonation performance. In a word, the 1:1 cocrystal model has the best comprehensive properties, is very promising, and worth more theoretical investigations and experimental tests. This paper gives some original theories to better understand the cocrystal mechanism and provides some helpful guidance and useful instructions to help design CL-20 cocrystal explosives.     

Growth morphology of CL-20/HMX cocrystal explosive: insights from solvent behavior under different temperatures

A 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) /1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)-isopropanol (IPA) interfacial model was constructed to investigate the effect of temperature on cocrystal morphology. A constant volume and temperature molecular dynamics (NVT-MD) simulation was performed on the interfacial model at various temperatures (295–355 K, 20 K intervals). The surface electrostatic potential (ESP) of the CL-20/HMX cocrystal structure and IPA molecule were studied by the B3LYP method at 6–311++G (d, p) level. The surface energies, polarities, adsorption energy, mass density distribution, radial distribution function (RDF), mean square displacement (MSD) and relative changes of attachment energy were analyzed. The results show that polarities of (1 0 0) and (0 1 1) cocrystal surfaces may be more negative and affected by IPA solvent. The adsorption energy per area indicates that growth of the (1 0–2) face in IPA conditions may be more limited, while the (1 0 0) face tends to grow more freely. MSD and diffusion coefficient (D) analyses demonstrated that IPA molecules gather more easily on the cocrystal surface at lower temperatures, and hence have a larger effect on the growth of cocrystal faces. RDF analysis shows that, with the increasing of temperature, the strength of hydrogen bond interactions between cocrystal and solvent becomes stronger, being highest at 335 K for the (1 0 0) and (0 1 1) interfacial models. Results of relative changes of modified attachment energy show that (1 0 0) and (0 1 1) faces tends to be larger than other faces. Moreover, the predicted morphologies at 295 and 355 K are consistent with experimental values, proving that the CL-20/HMX-IPA interfacial model is a reasonable one for this study.

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Graphical Abstract Construction of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) /1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)-isopropanol (IPA) interfacial model, analysis, and morphology prediction of cocrystal.

     

Investigation of the effect of the CAB/A3 system on HNIW-based PBXs using molecular dynamics

The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an attachment energy (AE) model to elucidate the HNIW surfaces that are present under real-world conditions. The simulation results were consistent with the experimentally derived ones, and they indicated that the exposed HNIW surfaces were (0 0 1), (1 1 0), and (1 1 ?1). The mechanical properties of CAB with different amounts of A3 were calculated at different temperatures, and the results showed that the amount of A3 was a stronger influence than the temperature on the mechanical properties. The binding energies between CAB/A3 and the exposed HNIW surfaces were calculated. Based on the binding energy and the area of each exposed surface, the weighted-average binding energy was calculated and then used instead of the total binding energy to evaluate the effect of the temperature and the A3 content on the binding energy. The average binding energy was found to be highest when the temperature was 313 K and the mass fraction of A3 was 0.15.     

Surface structures of oligoglycines: A molecular dynamics simulation

An atomistic molecular dynamics (MD) simulation of the adsorption of biantennary oligoglycine [H-Gly₄-NH(CH₂)₅]₂ onto a graphite and mica surface is described. The structure of the resultant adsorption layers is analyzed. The secondary structure motifs of peptide blocks are studied by the STRIDE (structural identification) and DSSP (dictionary of the secondary structure of proteins) methods. The results of the study confirm the possibility of forming a polyglycine-II (PGII) structure in the monolayers of biantennary oligoglycines (BAOG) on a graphite surface previously supposed from the data of atomic force microscopy.     

Structural investigation of syringomycin-E using molecular dynamics simulation and NMR

Syringomycin-E (SR-E) is a cyclic lipodepsinonapeptide produced by certain strains of the bacterium Pseudomonas syringae pv. syringae. It shows inhibitory effects against many fungal species, including human pathogens. Its primary biological target is the plasma membrane, where it forms channels comprised of at least six SR-E molecules. The high-resolution structure of SR-E and the structure of the channels are currently not known. In this paper, we investigate in atomic detail the molecular features of SR-E in water by NMR and in water and octane by molecular dynamics simulation (MD). We built a model of the peptide and examined its structure in water and octane in 200 ns MD simulations both with and without distance restraints derived from NMR NOE data. The resulting trajectories show good agreement with the measured NOEs and circular dichroism data from the literature and provide atomistic models of SR-E that are an important step toward a better understanding of the antifungal and antibacterial activity of this peptide.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Theoretical investigation of the safety of nitroguanidine-based PBXs containing the nonpolar desensitizing agent polytetrafluoroethylene

In order to elucidate why the inclusion of a nonpolar desensitizing agent in polymer-bonded explosives (PBXs) affects their sensitivity and safety, the intermolecular interactions between nitroguanidine (NQ: a high-energy-density compound used as a propellant and in explosive charges) and F₂C=CF₂ were investigated theoretically at the B3LYP/6–311++G(2df,2p) and M06-2X/6–311++G(2df,2p) levels of theory, focusing especially on the influence of intermolecular interactions on the strength of the trigger bond in NQ. The binding energies and mechanical properties of various β-NQ/polytetrafluoroethylene PBXs were also studied via molecular dynamics simulation. The results indicated that the weak intermolecular interactions between NQ and F₂C=CF₂ have almost no effect on the strength of the trigger bond or the energy barrier to the intramolecular hydrogen-transfer isomerization of NQ, as also confirmed by an AIM (atoms in molecules) analysis. However, the mechanical properties of the β-NQ/polytetrafluoroethylene PBXs were found to be significantly different from those of pure β-NQ: the PBXs showed reduced rigidity and brittleness, greater elasticity and plasticity, and—in particular—better ductility. Thus, β-NQ-based PBXs with polytetrafluoroethylene are predicted to be less sensitive to external mechanical stimuli, leading to reduced explosive sensitivity and increased safety.

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Only mechanical properties influence the safety of nitroguanidine-based PBXs

     

Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations

Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the diisocyanates and diols, in particular changes in the mesogen, were investigated. Introduction of mesogenic segments into the polymers suppresses the ordering. Stiff end substituents (phenyl and alkoxy groups) of the mesogens stabilize the mesophases to such an extent that the negative influence of long polymer chains is compensated and the liquid-crystalline properties are recovered. All-atom molecular dynamics simulations in the Cerius² modeling environment were carried out to characterize the structures of the polymers. Analysis of the dynamic trajectories at 20, 100, 120 and 170 °C revealed changes in conformation of macromolecules, which correlate with DSC measurements.Figure Example of structure relaxation of D4/TDI molecule at indicated simulation times (temperature 20 °C): a complete structure; b backbone structure; c top view of molecule     

Assessment of the DNA-binding properties of actinomycin and its derivatives by molecular dynamics simulation

A molecular dynamics simulation was used to assess the effect on the elasticity of a DNA fragment and the efficiency of DNA binding for actinomycins (antibiotics that are used in chemotherapy for certain oncology diseases). Hydroxyl and amino groups that were introduced as substituents in the phenoxazine ring of actinomycin were tested for their effect on the dynamic behavior and stability of antibiotic–DNA complexes. The Young modulus was calculated for DNA, DNA–actinomycin, DNA–7-hydroxyactinomycin, and DNA–7-aminoactinomycin. The free energy of complexation with DNA was calculated for actinomycin and its two analogs. The substituents were assumed to structurally stabilize the DNA fragment via additional hydrogen bonding.     

Assessment of the elastic properties of amorphous calcium silicates hydrates (I) and (II) structures by molecular dynamics simulation

Based on Hamid model of 11Å tobermorite, amorphous calcium silicates hydrates (or C-S-H) structures (Ca₄Si₆O₁₄(OH)₄?2H₂O as the C-S-H(I) and (CaO)_1.67(SiO₂)(H₂O)_1.75 as the C-S-H(II)) with the Ca/Si ratio of 0.67 and 1.7 are concerned. Then, as the representative ‘globule’ C-S-H, two amorphous C-S-H structures with the size of 5.352 × 4.434 × 4.556 nm³ during the stretch process are simulated at a certain strain rate of 10^?3 ps^?1 by LAMMPS program for molecular dynamics simulation, using ClayFF force field. The tensile stress–strain curves are obtained and analysed. Besides, elastic modulus of the ‘globule’ C-S-H is calculated to assess the elastic modulus of C-S-H phases (the low-density C-S-H – LD C-S-H – and the high-density C-S-H – HD C-S-H), where the porosity is a critical factor for explaining the relationship between ‘globule’ C-S-H at nanoscale and C-S-H phases at microscale. Results show that: (1) The C-S-H(I) structure has transformed from crystalline to amorphous during the annealing process, Young’s moduli in x, y and z directions are almost the same. Besides, the extent of aggregation and aggregation path for water molecules in the structure is different in three directions. (2) Young’s modulus of both amorphous C-S-H(I) and C-S-H(II) structures with a size of about 5 nm under strain rate of 10^?3 ps^?1 at 300 K in three directions is averaged to be equal, of which C-S-H(II) structure is about 60.95 GPa thus can be seen as the elastic modulus of the ‘globule’ C-S-H. (3) Based on the ‘globule’ C-S-H, the LD C-S-H and HD C-S-H can be assessed by using the Self-Consistent Scheme (separately 18.11 and 31.45 GPa) and using the Mori–Tanaka scheme (29.78 and 37.71 GPa), which are close to the nanoindentation experiments by Constantinides et al. (21.7 and 29.4 GPa).     

A comparison of the electromechanical properties of structurally diverse proteins by molecular dynamics simulation

Proteins are subjected to electric fields both within the cell and during routine biochemical analysis. We have used atomistic molecular dynamics simulations to study conformational changes within three structurally diverse proteins subjected to high electric fields. At electric fields in excess of .5?V/nm, major structural changes were observed in all three proteins due to charge redistribution within the biomolecule. However, the electromechanical resilience was found to be highly dependent on the protein secondary structure, with α-helices showing a particularly high susceptibility to deformation by the applied electric field.     

Thermostability of protein studied by molecular dynamics simulation

The thermostability of protein thermostable cathechol 2,3-dixoygenase (TC23O) has been studied by the parallel molecular dynamics simulations. By analysis of the exponent beta, which is related to the scattering spectrum and constant-pressure heat capacity Cp, we reveal the respective contribution of a specific residue 228 proline; a specific salt bridge, Lys188N-Glu291OE1; four ions; and a different water environment to the thermostability of TC23O. The dynamic transition temperature of the mutants, Pro228Ser and Glu291Gly of the TC23O, was decreased about 10 degrees C and 19 degrees C respectively. The displacement of the four ions had no significant effect on the thermostability of TC23O. Water affects the thermostability by influencing the changes of accessible conformation to a certain extent. All these results agree with the known experimental results.     

Structure and stability of the insulin dimer investigated by molecular dynamics simulation

Molecular dynamics simulation indicates that the dynamical behaviour of the insulin dimer is asymmetric. Atomic level knowledge of the interaction modes and protein conformation in the solvation state identifies dynamical structures, held by hydrogen bonds that stabilize, mainly in one monomer, the interaction between the chains. Dynamic cross-correlation analysis shows that the two insulin monomers behave asymmetrically and are almost independent. Solvation energy, calculated to evaluate the contribute of each interface residue to the dimer association pattern, well compares with the experimental association state found in protein mutants indicating that this parameter is an important factor to explain the association properties of mutated insulin dimers.     

A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties

Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Ku?erka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (D_B), hydrophobic thickness (D_C), and lipid volume (V_L). The only minor discrepancy between simulation and experiment is a measure of (D_B − D_HH) / 2 where D_HH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.     

Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation

A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.     

New potential inhibitors of mTOR: a computational investigation integrating molecular docking,virtual screening and molecular dynamics simulation

The mTOR (mammalian or mechanistic Target Of Rapamycin), a complex metabolic pathway that involves multiple steps and regulators, is a major human metabolic pathway responsible for cell growth control in response to multiple factors and that is dysregulated in various types of cancer. The classical inhibition of the mTOR pathway is performed by rapamycin and its analogs (rapalogs). Considering that rapamycin binds to an allosteric site and performs a crucial role in the inhibition of the mTOR complex without causing the deleterious side effects common to ATP-competitive inhibitors, we employ ligand-based drug design strategies, such as virtual screening methodology, computational determination of ADME/Tox properties of selected molecules, and molecular dynamics in order to select molecules with the potential to become non-ATP-competitive inhibitors of the mTOR enzymatic complex. Our findings suggest five novel potential mTOR inhibitors, with similar or better properties than the classic inhibitor complex, rapamycin.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation

A fully hydrated dimiristoylphosphatidylcholine (DMPC) bilayer has been studied by a molecular dynamics simulation. The system, which consisted of 64 DMPC molecules and 1792 water molecules, was run in the NVE ensemble at a temperature of 333 K for a total of 10 ns. The resulting trajectory was used to analyze structural and dynamical quantities. The electron density, bilayer spacing, and order parameters (S(CD)), based on the AMBER forcefield and SPCE water model are in good agreement with previous calculations and experimental data. The simulation reveals evidence for two types of lateral diffusive behavior: cage hopping and that of a two-dimensional liquid. The lateral diffusion coefficient is 8 x 10(-8) cm(2)/s. We characterize the rotational motion, and find that the lipid tail rotation (D(rot_tail) = -0.04 rad(2)/ns) is slower then the head group rotation (D(rot_hg) = 2.2 rad(2)/ns), which is slower than the overall in plane (D(rot) = 3.2 rad(2)/ns) for the lipid molecule.     

Effects of oxygenated sterol on phospholipid bilayer properties: a molecular dynamics simulation

The properties of dipalmitoylphosphatidylcholine (DPPC):6-ketocholestanol bilayer at 50 mol% sterol were studied using the molecular dynamics simulation technique. Our simulations were performed at constant pressure and temperature on a nanosecond time scale. Data from this simulation were compared to the results of our previous simulations on DPPC and DPPC-cholesterol bilayers. We conclude that the differences in the properties of membranes with cholesterol and ketocholestanol are due to the difference in 6-ketocholestanol and cholesterol location in the bilayer. The presence of the keto group in ketocholestanol moves the sterol towards the polar region closer to interface with water. We predict that similar mechanisms would govern the properties of membranes with other oxygenated sterols, such as for example 7-ketocholesterol. Results of our simulations are in a good agreement with the data available from the experiment.