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In situ monitoring of molecular aggregation using circular dichroism
摘要： The aggregation of molecules plays an important role in determining their function. Electron microscopy and other methods can only characterize the variation of microstructure, but are not capable of monitoring conformational changes. These techniques are also complicated, expensive and time-consuming. Here, we demonstrate a simple method to monitor in-situ and in real-time the conformational change of (R)-1,1′-binaphthyl-based polymers during the aggregation process using circular dichroism. Based on results from molecular dynamics simulations and experimental circular dichroism measurements, polymers with “open” binaphthyl rings are found to show stronger aggregation-annihilated circular dichroism effects, with more negative torsion angles between the two naphthalene rings. In contrast, the polymers with “locked” rings show a more restrained aggregation-annihilated circular dichroism effect, with only a slight change of torsion angle. This work provides an approach to monitor molecular aggregation in a simple, accurate, and efficient way.
关键词： molecular aggregation,binaphthyl-based polymers,conformational change,circular dichroism,molecular dynamics simulations
更新于2025-09-09 09:28:46
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Calculation of the Raman Q branch of hydrogen in water and comparison with experiments
摘要： Calculations of the Raman Q-branch line shifts and line widths of H2 in water at three different pressures and at 280 K are presented and compared with available experimental results. The calculations are based on a perturbative method in which the perturbation consists of those components of the H2–H2O interaction that depend on vibrational and/or rotational coordinates. In the unperturbed system the rotovibrational motion of the hydrogen molecule is separated from the dynamics of the rest of the system. The unperturbed rotovibrational motion of H2 is treated quantum mechanically whereas the dynamics of the rest of the system is calculated by classical molecular dynamics (MD). The MD calculations are repeated with two different models for the water–hydrogen potential energy. Both are Lennard-Jones models but in one the parameters are derived from the Lorentz–Bertholet combination rules and in the other they are taken from gas phase scattering data. The numerical results for the Raman Q-branch spectra are compared with the measurements in order to determine which model is more dependable.
关键词： molecular hydrogen in water,molecular dynamics,Raman spectroscopy
更新于2025-09-09 09:28:46
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Complexities of atomic structure at CdO/MgO and CdO/Al 2O 3 interfaces
摘要： We report the interface structures of CdO thin films on (001)-MgO and (0001)-Al2O3 substrates. Using aberration corrected scanning transmission electron microscopy, we show that epitaxial growth of (001)-CdO||(001)-MgO occurs with a lattice misfit greater than 10%. A high density of interface misfit dislocations is found to form. In combination with molecular dynamics simulations, we show that dislocation strain fields form and overlap in very thin heterostructures of CdO and MgO (< 3 nm). On the c-Al2O3 substrate, we find that CdO grows with a surface normal of [025]. We show that three rotation variants form due to the symmetry of the sapphire surface. These results contribute insights into the epitaxial growth of these rock-salt oxides.
关键词： CdO,epitaxial growth,Al2O3,scanning transmission electron microscopy,molecular dynamics simulations,MgO,interface structures
更新于2025-09-09 09:28:46
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Equi-biaxial compressive strain in graphene: Grüneisen parameter and buckling ridges
摘要： Here we report equi-biaxial compressive strain in monolayer graphene on SiO2 and Si3N4 substrates induced by thermal cycling in vacuum. The equi-biaxial strain is attributed to the mismatch in coefficient of thermal expansion between graphene and the substrate and sliding of graphene on the substrate. Importantly, the induced buckling ridges in graphene exhibit a pattern representing the symmetry of graphene crystal structure, which agreed well with our molecular dynamics (MD) simulations. Furthermore, these thermally-induced buckling ridges were found reminiscent of those in graphene synthesized by the CVD and SiC sublimation methods, suggesting the same origin of formation of the buckling ridges.
关键词： biaxial strain,thermal cycling,graphene,buckling ridges,molecular dynamics simulation,Grüneisen parameter
更新于2025-09-09 09:28:46
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Lattice Thermal Conductivity Calculation of Sb2Te3 using Molecular Dynamics Simulations
摘要： We study lattice thermal conductivity of Sb2Te3 using molecular dynamics simulations. The interatomic potentials are fitted to reproduce total energy and elastic constants, and phonon properties calculated using the potentials are in reasonable agreement with first-principles calculations and experimental data. Our calculated lattice thermal conductivities of Sb2Te3 decrease with temperature from 150 K to 500 K. The in-plane lattice thermal conductivity of Sb2Te3 is higher than cross-plane lattice thermal conductivity of Sb2Te3, as in the case of Bi2Te3, which is consistent with the anisotropy of the elastic constants.
关键词： Thermal conductivity,Interatomic potential,Molecular dynamics,Sb2Te3
更新于2025-09-09 09:28:46
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Molecular Dynamics Simulation on B3-GaN Thin Films under Nanoindentation
摘要： The B3-GaN thin film was investigated by performing large-scale molecular dynamics (MD) simulation of nanoindentation. Its plastic behavior and the corresponding mechanism were studied. Based on the analysis on indentation curve, dislocation density, and orientation dependence, it was found that the indentation depths of inceptive plasticity on (001), (110), and (111) planes were consistent with the Schmid law. The microstructure evolutions during the nanoindentation under different conditions were focused, and two formation mechanisms of prismatic loop were proposed. The “lasso”-like mechanism was similar to that in the previous research, where a shear loop can translate into a prismatic loop by cross-slip; and the extended “lasso”-like mechanism was not found to be reported. Our simulation showed that the two screw components of a shear loop will glide on another loop until they encounter each other and eventually produce a prismatic dislocation loop.
关键词： anisotropy,dislocation density,prismatic loops,B3-GaN,molecular dynamics
更新于2025-09-09 09:28:46
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Dynamical processes of low-energy carbon ion collision with the graphene supported by diamond
摘要： The dynamical processes of a low-energy carbon ion collision with the graphene sheet supported by diamond at three impact positions are studied by using empirical potential molecular dynamics simulations. The energy transformation and the structural evolution have been studied. Five types of processes are observed: adsorption, hybridization, defects formation in diamond, atom emission and transmission. We find that the irradiation damage is closely related to the incident energy and impact position. In our simulations, as the projectile collides at a graphene atom, it transfers most of its energy to the primary knock-on atom, and defects are created in graphene. When the projectile moves perpendicular towards the center of a C-C bond in the graphene sheet, the energy transferred from the projectile to the atoms associated with the bond increases firstly and then decreases with the increasing incident energy, and the graphene sheet remains two-dimensional crystal structure after collision when the incident energy is larger than 360 eV. While the impact location is the center of a hexagonal ring on the graphene sheet, the energy transferred from the projectile to the atoms of the target ring is very small regardless of how large is the incident energy, and the graphene sheet is able to keep perfect crystal structure when the incident energy is larger than 34 eV.
关键词： diamond,carbon ion collision,graphene,irradiation damage,molecular dynamics simulations
更新于2025-09-09 09:28:46
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Thermodynamic, transport, and optical properties of dense silver plasma calculated using the GreeKuP code
摘要： The transport and optical properties of a dense silver plasma are calculated using our parallel GreeKuP code. The code uses the results of Vienna ab initio simulation package (VASP) as input information and is based upon the Kubo–Greenwood formula. The calculation is performed at the normal density 10.5 g/cm3 and 3 kK ≤ T ≤ 20 kK. Under these conditions, the results are strongly influenced by the presence of the d-electrons in silver: the real part of dynamic electrical conductivity has a non-Drude shape, the temperature dependence of thermal conductivity is non-monotonic, and the Wiedemann–Franz law is violated.
关键词： transport and optical properties,Kubo–Greenwood formula,GreeKuP code,quantum molecular dynamics
更新于2025-09-09 09:28:46
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Investigation of Structure and Dynamics in a Photochromic Molecular Crystal by NMR Crystallography
摘要： A photochromic anil, N-(3,5-di-t-butylsalicylidene)-4-amino-pyridine, has been studied by single-crystal X-ray diffraction, multinuclear magic-angle spinning NMR and first-principles density functional theory (DFT) calculations. Interpretation of the solid-state NMR data on the basis of calculated chemical shifts confirms the structure is primarily composed of molecules in the ground-state enol tautomer, while thermally-activated cis-keto and photoisomerised trans-keto states exist as low-level defects with populations that are too low to detect experimentally. Variable temperature 13C NMR data reveals evidence for solid-state dynamics which is found to be associated with fast rotational motion of t-butyl groups and 180° flips of the pyridine ring, contrasting the time-averaged structure obtained by X-ray diffraction. Comparison of calculated chemical shifts for the full crystal structure and an isolated molecule also reveals evidence for an intermolecular hydrogen-bond involving the pyridine ring and an adjacent imine carbon which facilitates the flipping motion. The DFT calculations also reveal that the molecular conformation in the crystal structure is very close to the energetic minimum for an isolated molecule, indicating that the ring dynamics arise as a result of considerable steric freedom of the pyridine ring and which also allows the molecule to adopt a favourable conformation for photochromism.
关键词： NMR crystallography,photochromic,anil,solid-state NMR,DFT calculations,molecular dynamics
更新于2025-09-09 09:28:46
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Thermal conductivity of TiO<sub>2</sub> nanotube: A molecular dynamics study
摘要： The thermal conductivity of anatase TiO2 nanotubes was investigated using equilibrium molecular dynamics simulations based on Green-Kubo formalism. The calculated thermal conductivity of ~8.16 W/K ? m for anatase crystal at room temperature agrees well with experimental value of ~8.5 W/K?m, demonstrating that the method used in our calculation can provide a good description for the thermal transport of TiO2. The dependence of the thermal conductivity of TiO2 nanotubes with temperature, tube size and chirality were studied in detail. The relationship between the thermal conductivity and the vibrational density-of-states of the nanotubes was also investigated.
关键词： Molecular dynamics simulations,Thermal conductivity,Nanotube structure
更新于2025-09-09 09:28:46