Summary: We describe molecular dynamics simulations of α‐tetrathiophene molecules deposited on a flat graphite substrate, at two different temperatures (300 K and 400 K) and several degrees of coverage (from approximately one to three molecular layers). The simulations employ a modified version of the CFF91 force field, with the torsion parameters tailored on high‐level ab initio calculations on 2,2′‐bithiophene. We found that the molecules in the first layer were relatively planar and packed against the underlying surface, while those outside it were not arranged in well‐defined layers and were more conformationally disordered. On the time scale of the simulation, the molecules did not crystallize but rather achieved a liquid crystalline‐like state with their average director parallel to the surface.
Side view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer). 相似文献
The kinetics of NO adsorption and dissociation on Pd(111) surfaces and the NO sticking coefficient (s(NO)) were probed by isothermal kinetic measurements between 300 and 525 K using a molecular beam instrument. NO dissociation and N2 productions were observed in the transient state from 425 K and above on Pd(111) surfaces with selective nitrogen production. Maximum nitrogen production was observed between 475 and 500 K. It was found that, at low temperatures, between 300 and 350 K, molecular adsorption occurs with a constant initial s(NO) of 0.5 until the Pd(111) surface is covered to about 70-80% by NO. Then s(NO) rapidly decreases with further increasing NO coverage, indicating typical precursor kinetics. The dynamic adsorption - desorption equilibrium on Pd(111) was probed in modulated beam experiments below 500 K. CO titration experiments after NO dosing indicate the diffusion of oxygen into the subsurface regions and beginning surface oxidation at > or = 475 K. Finally, we discuss the results with respect to the rate-limiting character of the different elementary steps of the reaction system. 相似文献
Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K. 相似文献
The molecular dynamics method has been applied to simulate the melting temperatures of CaF 2 at elevated temperature and high pressure and to calculate the P～V equation of state of CaF 2 up to 100 GPa at 300 K. The interatomic potential was taken to be the sum of pairwise additive Coulomb, van der Waals attractions, and repulsive interactions. In addition, the shell model was used in molecular dynamics simulation. The pressure dependence of the melting temperature of CaF 2 was predicted up to 4 GPa. However, in order to account for the superheating melting of the molecular dynamic simulation, the simulated melting temperatures of CaF 2 were corrected by the modern theory of melting. Consequently, the melting temperatures of CaF 2 were accurately obtained at elevated temperature and high pressure. Therefore, it is shown that shell model molecular dynamics simulation at constant pressure indeed provides a useful tool for studying the melting temperatures of other materials under high pressures. 相似文献
Nitrogen equation of state at pressures up to 30 GPa (300 kbars) and temperatures above 800 K was studied by molecular dynamics (MD) simulations. The dynamics of the N(2) molecules is treated in hard rotor approximation, i.e., it accounts both translational and rotational degrees of freedom. The rotational motion of the N(2) molecule is treated assuming constant moment of inertia of the nitrogen molecule. The new MD program fully accounts anisotropic molecular nitrogen interaction. The N(2)-N(2) interaction potential has been derived by van der Avoird et al. [J. Chem. Phys. 84, 1629 (1986)] using the results of high precision Hartree-Fock ab initio quantum mechanical calculations. The potential, fully accounts rotational symmetry of the N(2)-N(2) system, by employing 6-j Wigner symbols, i.e., preserving full rotational symmetry of the system. Various numerical algorithms were tested, in order to achieve the energy preservation during the simulation. It has been demonstrated that the standard Verlet algorithm was not preserving the energy for the standard MD time step, equal to 5x10(-16) s. Runge-Kutta fourth order method was able to preserve the energy within 10(-4) relative error, but it requires calculation of the force four times for each time step and therefore it is highly inefficient. A predictor-corrector method of the fifth order (PC5) was found to be efficient and precise and was therefore adopted for the simulation of the molecular nitrogen properties at high pressure. Singer and Fincham algorithms were tested and were found to be as precise as PC5 algorithm and they were also used in the simulation of the equation of state. Results of MD simulations are in very good agreement with the experimental data on nitrogen equation of state at pressures below 1 GPa (10 kbars). For higher pressures, up to 30 GPa (300 kbars), i.e., close to molecular nitrogen stability limit, determined by Nellis et al. [Phys. Rev. Lett. 85, 1262 (1984)], the obtained numerical results provide new data of the experimentally unexplored region. These data were formulated in the analytical form of pressure-density-temperature equation of state. 相似文献
The equation of state of MgSiO3 perovskite under high pressure and high temperature is simulated using the molecular dynamics method. It was found that the molecular dynamics simulation is very successful in accurately reproducing the measured molar volumes of MgSiO3 perovskite over a wide range of temperatures and pressures. The simulated equation of state of MgSiO3 perovskite matched experimental data at up to 140GPa at 300 K, as well as the fitting data of others and results from the first-principles simulation based on the local density approximation. The simulated equations of state of MgSiO3 perovskite at higher temperatures and higher pressures also correspond to the other calculations. In addition, the volume compression data of MgSiO3 perovskite is simulated up to 120 GPa at 300, 900, 2000 and 3000 K, respectively. 相似文献
The folding behavior of five different amine-functionalized m-poly(phenyleneethynylene) (m-PPE) oligomers containing 24 phenyl rings (12 residues, where a residue includes 2 phenyl rings) in water was examined by using a combination of molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulation techniques. The REMD method employed the highly parallelized GROMACS MD software and a modified OPLS-AA force field to simulate 44 replicas of each solvated system in parallel, with temperatures ranging from 300 to 577 K. Our results showed that the REMD method was more effective in predicting the helical conformation of the m-PPE in water, from an extended structure, than canonical MD methods in the same simulation time. Furthermore, we observed from canonical MD simulations of the explicitly solvated helical m-PPEs at 300 K that the radius of gyration, average helix inner diameter, and average helix pitch of the helical structure all pass through a minima when the side group is R = OC(2)H(5) as R is changed from R = H through OC(4)H(9). 相似文献
The local structure of quenching process of lithium chloride has been studied by molecular dynamics simulation. The sequentially-quenched model was adapted. When the equilibrium reached at the melting point 878 K, the system was fastly quenched to 698 K and then the system relaxed to equilibrium. The process was repeated as above and the system was quenched to 498 K, 298 K, and 198 K, respectively, We calculated the quadratic invariants Q_l histograms at different temperatures by averaging the Q_l values of theinstantaneous configurations with the method of fond spherical harmonics statistics under equal neighbor number. Consulting the Q_l histograms of the linear combination model with a parameter of square deviation in which model the local diamond structure was predominant, we found that the Q_l histograms from the model and those from the simulation were very similar. The results showed that in the quenched LiCl system the local orientation obviously tended to be binary diamond structure (like GaAs) and the square deviation in model would be decreased with the lowering of simulation temperature. 相似文献
