Car-parrinello molecular dynamics simulation of liquid formic acid

First-principles molecular dynamics has been used to investigate the structural, vibrational, and energetic properties of formic acid, formic acid-formate anion dimers, and liquid formic acid in a periodically repeated box with 32 formic acid molecules. We found that in liquid formic acid the hydrogen-bonded clusters mainly consist of linear branching chains. From our simulation, we got good agreement with the available structural and dynamical data. We also studied the proton transfer in the cis-formic acid-formate anion dimer, and we showed that this proton transfer does not have any potential barrier. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed.     

MPSA effects on copper electrodeposition investigated by molecular dynamics simulations

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates the copper-ion association with MPSA. The model also was used to simulate induced-charge effects and adsorption on a nonplanar electrode surface.     

Kinetics of NaCl nucleation in supercritical water investigated by molecular dynamics simulations

At system pressures between 17 MPa and 25 MPa the nucleation and growth of NaCl nanoparticles in water at supercritical conditions was investigated by molecular dynamics simulations at different system temperatures and system densities. Our results show that particle formation takes place within a few hundred picoseconds after the jump from ambient to supercritical conditions. After nucleation a phase of growth by adding monomers is followed by growth via cluster-cluster collisions. We present results on the time development of distributions of cluster sizes, cluster compositions, and cluster temperatures as well as radial distribution functions and nucleation rates.     

Explicit proton transfer in classical molecular dynamics simulations

We present Hydrogen Dynamics (HYDYN), a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, from the special pair dance, to the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the first solvation layer. Advantages of HYDYN with respect to existing methods are computational efficiency, microscopic reversibility, and easy parameterization for any force field. © 2014 Wiley Periodicals, Inc.     

Energy conservation in molecular dynamics simulations of classical systems

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.     

Aggregation of FeCl2 clusters in supercritical water investigated by molecular dynamics simulations

We have carried out molecular dynamics (MD) simulations of the aggregation of FeCl 2 clusters in supercritical water. The particle formation in systems of 2048 water molecules (rigid SPC/E-model) and 120 Fe (2+) ions and 240 Cl (-) ions has been investigated for 250 ps at five different state points at temperatures from 798 to 873 K and system densities from 0.18 g/cm (3) to 0.13 g/cm (3). We describe the particle growth by means of properties of the largest cluster in a system as well as cluster size averaged and time averaged observables. From preexisting or immediately formed units of Fe (2+)-Cl (-), Fe (2+)-Cl (-) 2, Fe (2+)-Cl (-) 3 etc., the further growth of clusters is dominated by aggregation of such small building blocks. Clusters up to 10 ions in size with large charge imbalances are found during the growth process while a balanced positive to negative charge ratio is found on the average with time and cluster size development. Water molecules are found within the FeCl 2 clusters during the whole time interval covered by the simulations, which is in agreement with the existence of crystal water in FeCl 2 crystals grown from aqueous solutions. The radial distribution functions obtained from the simulation data are in good agreement with experimental results of slightly distorted FeCl 2.4H 2O crystals.     

Structure and dynamics of N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ionic liquid from molecular dynamics simulations

Molecular dynamics (MD) simulations were performed on N-methyl-N-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide (mppy+TFSI-) from 303 to 393 K to improve understanding of the structure and ion transport of this ionic liquid. The density, ion self-diffusion coefficients, conductivity, and viscosity of mppy+TFSI- predicted from MD simulations are in good agreement with experimental measurements. The time-dependent shear modulus of the ionic liquids was calculated and compared with that for nonionic liquids. On average each mppy+ cation was found to be coordinated by four TFSI- anions. The angular distributions of N(TFSI-)-N(mppy+)-N(TFSI-) and N(mppy+)-N(TFSI-)-N(mppy+) exhibit a maximum at 80-90 degrees and a second maximum at 180 degrees . Correlation of ion motion was found to lower ionic conductivity by approximately one-third from the expected value based upon ion self-diffusion coefficients. Rotational motion of the cation and anion are anisotropic with the degree of anisotropy increasing with decreasing temperature. Electrostatic interactions are responsible for slowing down the dynamics of the ionic liquid by more than an order of magnitude and a dramatic decrease of the time-dependent shear modulus.     

第一原理分子动力学研究类金刚石薄膜的结合强度与摩擦性能

金刚石(110)表面具有不同方向上抛光速率的强烈不对称的特征,用第一性原理全能量平面波赝势方法模拟研究了类金刚石薄膜表面的结合强度与摩擦性能,确定了相互作用模型以及排斥力作用范围,研究了范德华排斥力在摩擦表面上的分布,研究结果表明,摩擦表层感受到的力在〈001〉和〈110〉2个方向上表现明显不同,而且〈110〉方向上摩擦力一直高于〈001〉方向上的摩擦力.     

Intermolecular polarizability dynamics of aqueous formamide liquid mixtures studied by molecular dynamics simulations

A molecular dynamics simulation study is presented for the relaxation of the polarizability anisotropy in liquid mixtures of formamide and water, using a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors of the molecules, and the dipole-quadrupole polarizability of water species. The long time diffusive decay of the collective polarizability anisotropy correlations exhibits a substantial slowing down as the formamide mole fraction increases in the mixture. The diffusive times for the polarizability relaxation obtained from the authors' simulations are in good agreement with optical Kerr effect experimental data, and they are found to correlate nearly linearly with the estimated mean lifetimes of the hydrogen bonds within the mixture, suggesting that the relaxation of the hydrogen bond network is responsible to some extent for the collective relaxation of the polarizability anisotropy of the mixture. The short time behavior of the polarizability anisotropy relaxation was investigated by computing the nuclear response function, R(t), which is very rapidly dominated by the formamide contribution as it is added to water, due to the much larger polarizability anisotropy of formamide molecules compared to that of water. Several contributions to the Raman spectrum were also analyzed as a function of composition, and the dynamical origin of the different bands was determined.     

Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations

We report the sum frequency generation (SFG) spectra of aqueous sodium iodide interfaces computed with the methodology outlined by Morita and Hynes (J. Phys. Chem. B 2002, 106, 673), which is based on molecular dynamics simulations. The calculated spectra are in qualitative agreement with experiment. Our simulations show that the addition of sodium iodide to water leads to an increase in SFG intensity in the region of 3400 cm(-1), which is correlated with an increase in ordering of hydrogen-bonded water molecules. Depth-resolved orientational distribution functions suggest that the ion double layer orders water molecules that are approximately one water layer below the Gibbs dividing surface. We attribute the increase in SFG intensity to these ordered subsurface water molecules that are present in the aqueous sodium iodide/air interfaces but are absent in the neat water/air interface.     

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations

The i‐motif tetrameric structure is built up from two parallel duplexes intercalated in a head‐to‐tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i‐motif structure, one with outermost 3′ extremities and the other with outermost 5′ extremities, called the 3′E and 5′E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3′E and 5′E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3′E topology of the [d(C2)]4 is much more stable than the 5′E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i‐motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i‐motif stability, is produced by a similar and non‐negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5′E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright © 2002 John Wiley & Sons, Ltd.     

Ab initio molecular dynamics simulations of the liquid/vapor interface of sulfuric acid solutions

Ab initio molecular dynamics simulations of the liquid-vapor interface are presented for thin slabs of 72 water molecules containing a single molecule of sulfuric acid. Trajectories in the 306-330 K range are calculated for two functionals with double- and triple-ζ quality basis sets. Comparisons are made between BLYP and HCTH/120 results for the slab simulations and for bulk simulations of one H(2)SO(4) in a periodic box with 63 waters. Good agreement is found with the available experimental data and the results of other relevant AIMD studies with respect to ionization of the acid, size of the coordination shells, partitioning of the ions with the hydronium exhibiting a surface preference and the anions in the interior, and the orientational distributions for the hydronium ions and for the surface/subsurface water molecules. The major differences in the performance of the two functionals are attributable to the greater basicity of the anion oxygen atoms with the HCTH functional and the more structured aqueous solution with BLYP. The enhanced basicity results in larger aqueous coordination shells for the anion oxygens. The structuring of the BLYP aqueous solution is observed in the corrugation of the water density profile, the higher first peak in g(OO)(r), and a smaller water self-diffusion constant. This structuring with the BLYP functional yields anion hydrogen bonds that endure longer and where the dissociated ions more rapidly and directly segregate in the slab. The simulations indicate that aqueous surfaces containing ionizable diprotic acids can be modeled with rather modest sized systems and be informative.     

Structure and dynamics of N,N-diethyl-N-methylammonium triflate ionic liquid, neat and with water, from molecular dynamics simulations

We investigated by means of molecular dynamics simulations the properties (structure, thermodynamics, ion transport, and dynamics) of the protic ionic liquid N,N-diethyl-N-methylammonium triflate (dema:Tfl) and of selected aqueous mixtures of dema:Tfl. This ionic liquid, a good candidate for a water-free proton exchange membrane, is shown to exhibit high ion mobility and conductivity. The radial distribution functions reveal a significant long-range structural correlation. The ammonium cations [dema](+) are found to diffuse slightly faster than the triflate anions [Tfl](-), and both types of ions exhibit enhanced mobility at higher temperatures, leading to higher ionic conductivity. Analysis of the dynamics of ion pairing clearly points to the existence of long-lived contact ion pairs. We also examined the effects of water through characterization of properties of dema:Tfl-water mixtures. Water molecules replace counterions in the coordination shell of both ions, thus weakening their association. As water concentration increases, water molecules start to connect with each other and then form a large network that percolates through the system. Water influences ion dynamics in the mixtures. As the concentration of water increases, both translational and rotational motions of [dema](+) and [Tfl](-) are significantly enhanced. As a result, higher vehicular ionic conductivity is observed with increased hydration level.     

The plastic and liquid phases of CCl3Br studied by molecular dynamics simulations

We present a molecular dynamics study of the liquid and plastic crystalline phases of CCl(3)Br. We investigated the short-range orientational order using a recently developed classification method and we found that both phases behave in a very similar way. The only differences occur at very short molecular separations, which are shown to be very rare. The rotational dynamics was explored using time correlation functions of the molecular bonds. We found that the relaxation dynamics corresponds to an isotropic diffusive mode for the liquid phase but departs from this behavior as the temperature is decreased and the system transitions into the plastic phase.     

Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations

A method is presented to interpolate the potential energy function for a part of a system consisting of a few degrees of freedom, such as a molecule in solution. The method is based on a modified finite element (FE) interpolation scheme. The aim is to save computer time when expensive methods such as quantum-chemical calculations are used to determine the potential energy function. The expensive calculations are only carried out if the molecule explores new unknown regions of the conformation space. If the molecule resides in regions previously explored, a cheap interpolation is performed instead of an expensive calculation, using known neighboring points. We report the interpolation techniques for the energies and the forces of the molecule, the handling of the FE mesh, and an application to a simple test example in molecular dynamics (MD) simulations. Good performance of the method was obtained (especially for MD simulations with a preceding Monte Carlo mesh generation) without losing accuracy. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1484–1495, 1997