Classical Molecular Dynamics Calculations Research Articles

Simple bond-order-type interatomic potential for an intermixed Fe-Cr-C system of metallic and covalent bondings in heat-resistant ferritic steels

It is known that M23C6(M = Cr/Fe) behavior in heat-resistant ferritic steels affects the strength of the material at high temperature. The ability to garner direct information regarding the atomic motion using classical molecular dynamics simulations is useful for investigating the M23C6 behavior in heat-resistant ferritic steels. For such classical molecular dynamics calculations, a suitable interatomic potential is needed. To satisfy this requirement, an empirical bond-order-type interatomic potential for Fe-Cr-C systems was developed because the three main elements to simulate the M23C6 behavior in heat-resistant ferritic steels are Fe, Cr, and C. The angular-dependent term, which applies only in non-metallic systems, was determined based on the similarity between a Finnis-Sinclair-type embedded-atom-method interatomic potential and a Tersoff-type bond-order potential. The potential parameters were determined such that the material properties of Fe-Cr-C systems were reproduced. These properties include the energy and lattice constants of 89 crystal structures; the elastic constants of four realistic precipitates; the bulk moduli of B1, B2, and B3 crystals; the surface energies of B1 and B2 crystals; and the defect-formation energies and atomic configurations of 66 Fe-Cr-C complexes. Most of these material properties were found to be reproduced by our proposed empirical bond-order potentials. The formation energies and lattice constants of randomly mixed Fe-Cr alloys calculated using the interatomic potentials were comparable to those obtained through experiments and first-principles calculations. Furthermore, the energies and structures of interfaces between Cr carbide and α-Fe as predicted through first-principles calculations were well reproduced using these interatomic potentials.

Interaction of a long alkyl chain protic ionic liquid and water.

A combined experimental/theoretical approach has been used to investigate the role of water in modifying the microscopic interactions characterizing the optical response of 1-butyl-ammonium nitrate (BAN) water solutions. Raman spectra, dominated by the signal from the protic ionic liquid, were collected as a function of the water content, and the corresponding spatial organization of the ionic couples, as well as their local arrangement with water molecules, was studied exploiting classical molecular dynamics calculations. High quality spectroscopic data, combined with a careful analysis, revealed that water affects the vibrational spectrum BAN in solution: as the water concentration is increased, peaks assigned to stretching modes show a frequency hardening together with a shape narrowing, whereas the opposite behavior is observed for peaks assigned to bending modes. Calculation results clearly show a nanometric spatial organization of the ionic couples that is not destroyed on increasing the water content at least within an intermediate range. Our combined results show indeed that small water concentrations even increase the local order. Water molecules are located among ionic couples and are closer to the anion than the cation, as confirmed by the computation of the number of H-bonds which is greater for water-anion than for water-cation. The whole results set thus clarifies the microscopic scenario of the BAN-water interaction and underlines the main role of the extended hydrogen bond network among water molecules and nitrate anions.

Isolated line shapes of molecular oxygen: Requantized classical molecular dynamics calculations versus measurements

We present comparisons between measured isolated line shapes of molecular oxygen in air at various pressures and those calculated, free of any adjusted parameter, using requantized classical molecular dynamics simulations (rCMDS). The measurements have been made for the R1Q2, P9P9, P11P11, P13P13, and P15Q14 transitions in the ${\mathrm{O}}_{2}$ singlet-\ensuremath{\Delta} band [$a\phantom{\rule{0.16em}{0ex}}{}^{1}{\ensuremath{\Delta}}_{g}\ensuremath{\leftarrow}X\phantom{\rule{0.16em}{0ex}}{}^{3}{\ensuremath{\Sigma}}_{g}^{\ensuremath{-}}(0,0)$] by the frequency-stabilized cavity ring-down spectroscopy technique. This work extends a previous study made for a single oxygen line [Phys. Rev. A 87, 032510 (2013)] and confirms the quality of this theoretical approach over broad ranges of pressure and rotational quantum number. Indeed, not only the collisional broadening coefficients but also the (small) deviations of observed line shapes with respect to the Voigt profile are accurately predicted. These results illustrate the viability of using the rCMDS method as a benchmark for the development and testing of simpler parametrized line profiles that are suitable for the analysis of underlying physical mechanisms and for atmospheric remote sensing applications.

Separation of photo-induced radical pair in cryptochrome to a functionally critical distance

Cryptochrome is a blue light receptor that acts as a sensor for the geomagnetic field and assists many animals in long-range navigation. The magnetoreceptor function arises from light-induced formation of a radical pair through electron transfer between a flavin cofactor (FAD) and a triad of tryptophan residues. Here, this electron transfer is investigated by quantum chemical and classical molecular dynamics calculations. The results reveal how sequential electron transfer, assisted by rearrangement of polar side groups in the cryptochrome interior, can yield a FAD-Trp radical pair state with the FAD and Trp partners separated beyond a critical distance. The large radical pair separation reached establishes cryptochrome's sensitivity to the geomagnetic field through weakening of distance-dependent exchange and dipole-dipole interactions. It is estimated that the key secondary electron transfer step can overcome in speed both recombination (electron back-transfer) and proton transfer involving the radical pair reached after primary electron transfer.

AC/AB Stacking Boundaries in Bilayer Graphene

Boundaries, including phase boundaries, grain boundaries, and domain boundaries, are known to have an important influence on material properties. Here, dark-field (DF) transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) imaging are combined to provide a full view of boundaries between AB and AC stacking domains in bilayer graphene across length scales from discrete atoms to the macroscopic continuum. Combining the images with results obtained by density functional theory (DFT) and classical molecular dynamics calculations, we demonstrate that the AB/AC stacking boundaries in bilayer graphene are nanometer-wide strained channels, mostly in the form of ripples, producing smooth low-energy transitions between the two different stackings. Our results provide a new understanding of the novel stacking boundaries in bilayer graphene, which may be applied to other layered two-dimensional materials as well.

Origins of the solvent effect on the propagation kinetics of acrylic acid and methacrylic acid

AbstractIn this study, the relative rate of polymerization of acrylic acid (AA) versus methacrylic acid (MAA) and the effect of water on the polymerization kinetics are investigated within a combined static and molecular dynamics set of computational tools. Experimentally the relative rate of propagation of AA versus MAA is around 35 in bulk and 31 in water. Classical Molecular Dynamics calculations have been carried out to determine the location of the solvent molecules in the proximity of the dimeric poly(AA) and poly(MAA) units. A combined implicit/explicit solvent model was used for the evaluation of the kinetics of the dimeric polymer chains. We show that the rate acceleration of both polymers in water is mainly due to entropic rather than electrostatic effects and is in agreement with experimental findings. Moreover the slower propagation rate of MAA versus AA is ascribed to additional steric effects present in MAA due to the methyl group at the α position of the monomer. Among the functionals used, the M06‐2X/6‐311+G(3df,2p)//B3LYP/6‐31+G(d) methodology reproduces the experimental rate constants quantitatively the best. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013

Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π-stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Atomistic modelling of friction of Cu and Au nanoparticles adsorbed on graphene

We present classical molecular dynamics calculations of the behavior of copper and gold nanoparticles on a graphene sheet, sheared with a constant applied force $F_{\rm a}$. The force $F_{\rm s}$ acting on the particle from the substrate depends on the material of the nanoparticles (Au or Cu), and exhibits a sawtooth dependency on time, which we attribute to local commensurability between the metal nanoparticle surface atomic positions with the graphene lattice. The time-averaged value of $F_{\rm s}$ (the friction force) acting on Au nanoparticles increases linearly with the contact area, having slopes close to the experimentally observable ones. A qualitative model is proposed to explain the observed results.

Diffusion dynamics of lithium ion and atom on graphene surfaces

Recent theoretical studies of the diffusion dynamics of lithium ions and atoms (Li + and Li) in carbon materials have been reviewed. Graphene, graphene flakes, and fullerene (C 60 ) were examined as the carbon materials. The direct ab initio molecular dynamics (MD) method, used in the present study, is a hybrid technique composed of ab initio molecular orbital and MD methods. The diffusion of Li + ions (atoms) and their interaction with the carbon materials are treated at the quantum mechanical level. The diffusion path and reaction mechanism obtained by the direct ab initio MD method were significantly different from those of a usual classical MD calculation. Details of the diffusion dynamics of the lithium were discussed on the basis of theoretical results.

Transport properties of room-temperature ionic liquids from classical molecular dynamics

Room-temperature ionic liquids (RTILs) have attracted much attention in the scientific community in the past decade due their novel and highly customizable properties. Nonetheless, their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics calculations are reported. Here, in particular, bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g., system-size effects or the choice of the interaction potential, is analyzed in detail.

Predicted structure, thermo-mechanical properties and Li ion transport in LiAlF4 glass

Materials with the LiAlF4 composition are of interest as protective electrode coatings in Li ion battery applications due to their high cationic conductivity. Here classical molecular dynamics calculations are used to produce amorphous model structures by simulating a quench from the molten state. These are analysed in terms of their individual pair correlation functions and atomic coordination environments. This indicates that amorphous LiAlF4 is formed of a network of corner sharing AlF6 octahedra. Li ions are distributed within this network, primarily associated with non-bridging fluorine atoms. The nature of the octahedral network is further analysed through intra‐ and interpolyhedral bond angle distributions and the relative populations of bridging and non-bridging fluorine ions are calculated. Network topology is considered through the use of ring statistics, which indicates that, although topologically well connected, LiAlF4 contains an appreciable number of corner‐linked branch‐like AlF6 chains. Thermal expansion values are determined above and below the predicted glass transition temperature of 1340K. Finally, movement of Li ions within the network is examined with predictions of the mean squared displacements, diffusion coefficients and Li ion activation energy. Different regimes for lithium ion movement are identified, with both diffusive and sessile Li ions observed. For migrating ions, a typical trajectory is illustrated and discussed in terms of a hopping mechanism for Li transport.

Y:BaZrO3 Perovskite Compounds II: Designing Protonic Conduction by using MD Models

The proton dynamics in Y-doped BaZrO(3) derivatives, in particular the different dopant environments within a Pm3m cubic framework, were studied by using classical molecular dynamics (MD) calculations. Single- and double substitution of zirconium by yttrium atoms was considered. The presence of yttrium induced variations in the surrounding oxygen sites, according to their local geometrical arrangements. The differences among such distinct oxygen sites became evident when protons interacted with them and upon changes in the temperature. So, different proton transfer pathways, which had different energy barriers, characterized the topologically different oxygen sites. The experimental proton-hopping activation energy was only reproduced in those structures in which two yttrium atoms formed a Y-O-Y arrangement, which also acted as multilevel protonic traps. Protonic conduction in these materials could be improved by avoiding such yttrium clustering, hence preventing the formation of the protonic traps.

Dissociative and non-dissociative adsorption dynamics of N2 on Fe(110)

We study the adsorption dynamics of N(2) on the Fe(110) surface. Classical molecular dynamics calculations are performed on top of a six-dimensional potential energy surface calculated within density functional theory. Our results show that N(2) dissociation on this surface is a highly activated process that takes place along a very narrow reaction path with an energy barrier of around 1.1 eV, which explains the measured low reactivity of this system. By incorporating energy exchange with the lattice in the dynamics, we also study the non-dissociative molecular adsorption process. From the analysis of the potential energy surface, we observe the presence of two distinct N(2) adsorption wells. Our dynamics calculations show that the relative population of these adsorption sites varies with the incident energy of the molecule and the surface temperature. We find an activation energy of around 150 meV that prevents molecular adsorption under thermal and hypothermal N(2) gas exposure of the surface. This finding is also consistent with the available experimental information.

Oxygen diffusion mechanism in the mixed ion-electron conductor NdBaCo2O5+x

Double perovskite cobaltites were recently presented as promising cathode materials for solid oxide fuel cells. While an atomistic mechanism was proposed for oxygen diffusion in this family of materials, no direct experimental proof has been presented so far. We report here the first study that directly compares experimental and theoretical diffusion pathways of oxygen in an oxide, namely in the double cobaltite compound, NdBaCo2O5+x. Model-free experimental nuclear density maps are obtained from the maximum entropy method combined with Rietveld refinement against high resolution neutron diffraction data collected at 1173 K. They are then compared to theoretical maps resulting from classical molecular dynamics calculations. The analysis of 3D maps of atomic densities allows identifying unambiguously the pathways and the mechanisms involved in the oxide ion diffusion. It is shown that oxygen diffusion occurs along a complex trajectory between Nd- and Co-containing a,b planes. The study also reveals that Ba-containing planes act as a barrier for oxygen diffusion. The diffusion mechanism is also supported through the oxygen sites occupancy analysis that confirms the increase of oxygen vacancies in the cobalt-planes on heating. The use of such combined experimental and theoretical analysis should be considered as a very powerful approach for materials design.

Controlling the tacticity in the polymerization of N-isopropylacrylamide: A computational study

In this study, the effect of alcohols as solvents on the kinetics and the tacticity of poly(N-Isopropylacrylamide) (PNIPAM) is investigated with a combined static and molecular dynamics set of computational tools. Classical molecular dynamics calculations have been carried out to determine the location of the solvent molecules in the proximity of the monomer and the dimer. A combined implicit/explicit solvent model was used for the evaluation of the kinetics of the dimeric polymer chains. Rate constants are calculated with the B3LYP/6-311 + G(d,p)//B3LYP/6-31 + G(d), BMK/6-311 + G(d,p)//B3LYP/6-31 + G(d), and MPWB1K/6-311 + G(d,p)//B3LYP/6-31 + G(d) methodologies via the standard transition state theory. We show that due to the proximity of the –NH and carbonyl groups on the syndiotactic propagating dimeric and trimeric chains, the alcohol can stabilize the corresponding transition states by forming a bridge between these functionalities and accelerate this path more than its isotactic counterpart. In agreement with experiment, the increase in the syndiotactic PNIPAM and the acceleration of the reaction in the presence of t-BuOH is predicted with all the DFT functionals utilized in this study.

Modeling Radiation Effects on the Fracture Process in Simplified Nuclear Glass

Experimentally, the evolution of several mechanic properties (hardness, density, Young’s modulus, fracture toughness) is observed in nuclear glasses under irradiation. In this work, classical molecular dynamics calculations are performed to better understand fracture mechanisms in simplified nuclear glasses at atomistic scale and to explain the radiation effects. Fractures are simulated in more disordered glasses, representative of irradiated samples, to reveal radiation effects. We observe a lower elastic limit and a greater plasticity in the irradiated glass that can explain its larger fracture toughness.

Dissociation of H2NCH Dication in a Strong Laser Field

Ab initio classical molecular dynamics calculations have been used to simulate the dissociation of H(2)NCH(2+) in a strong laser field. The frequencies of the continuous oscillating electric field were chosen to be ω = 0.02, 0.06, and 0.18 au (2280, 760, and 253 nm, respectively). The field had a maximum strength of 0.03 au (3.2 × 10(13) W cm(-2)) and was aligned with the CN bond. Trajectories were started with 100 kcal/mol of vibrational energy above zero point and were integrated for up to 600 fs at the B3LYP/6-311G(d,p) level of theory. A total of 200 trajectories were calculated for each of the three different frequencies and without a field. Two dissociation channels are observed: HNCH(+) + H(+) and H(2)NC(+) + H(+). About one-half to two-thirds of the H(+) dissociations occurred directly, while the remaining indirect dissociations occurred at a slower rate with extensive migration of H(+) between C and N. The laser field increased the initial dissociation rate by a factor of ca. 1.4 and decreased the half-life by a factor of ca. 0.75. The effects were similar at each of the three frequencies. The HNCH(+) to H(2)NC(+) branching ratio decreased from 10.6:1 in the absence of the field to an average of 8.4:1 in the laser field. The changes in the rates and branching ratios can be attributed to the laser field lowering the reaction barriers as a result of a difference in polarizability of the reactant and transition states.

Confined water inside single-walled carbon nanotubes: Global phase diagram and effect of finite length

Studies on confined water are important not only from the viewpoint of scientific interest but also for the development of new nanoscale devices. In this work, we aimed to clarify the properties of confined water in the cylindrical pores of single-walled carbon nanotubes (SWCNTs) that had diameters in the range of 1.46 to 2.40 nm. A combination of x-ray diffraction (XRD), nuclear magnetic resonance, and electrical resistance measurements revealed that water inside SWCNTs with diameters between 1.68 and 2.40 nm undergoes a wet-dry type transition with the lowering of temperature; below the transition temperature T(wd), water was ejected from the SWCNTs. T(wd) increased with increasing SWCNT diameter D. For the SWCNTs with D = 1.68, 2.00, 2.18, and 2.40 nm, T(wd) obtained by the XRD measurements were 218, 225, 236, and 237 K, respectively. We performed a systematic study on finite length SWCNT systems using classical molecular dynamics calculations to clarify the effect of open ends of the SWCNTs and water content on the water structure. It was found that ice structures that were formed at low temperatures were strongly affected by the bore diameter, a = D - σ(OC), where σ(OC) is gap distance between the SWCNT and oxygen atom in water, and the number of water molecules in the system. In small pores (a < 1.02 nm), tubule ices or the so-called ice nanotubes (ice NTs) were formed irrespective of the water content. On the other hand, in larger pores (a > 1.10 nm) with small water content, filled water clusters were formed leaving some empty space in the SWCNT pore, which grew to fill the pore with increasing water content. For pores with sizes in between these two regimes (1.02 < a < 1.10 nm), tubule ice also appeared with small water content and grew with increasing water content. However, once the tubule ice filled the entire SWCNT pore, further increase in the water content resulted in encapsulation of the additional water molecules inside the tubule ice. Corresponding XRD measurements on SWCNTs with a mean diameter of 1.46 nm strongly suggested the presence of such a filled structure.

Temperature-dependent properties of 147- and 309-atom iron-gold nanoclusters

The properties of several AuN and AuN−xFex nanoclusters are obtained by means of classical molecular dynamics calculations. In particular we study the configurations Au147, Au134Fe13, Au309, and Au254Fe55, which correspond to icosahedral magic numbers, for both the gold and the iron. We investigate the melting and freezing processes, atomic diffusion, hardness, vibration spectra, and specific heat of these nanoclusters. All the data obtained point toward the stability of the AuN−xFex system, with the gold atoms on the outside of the iron core.

Development of a Software to Optimize Parameters of Interatomic Potentials for Solid Systems

Generally, it is difficult to develop practical interatomic potentials which can be used in classical molecular dynamics calculations, since a method for development had not been established. In order to solve such problems, we had proposed a framework to develop interatomic potentials. However, the framework had not been widely used due to the difficulty of coding a process to optimize potential-parameters, which was involved in the framework. In this work, a practical software to optimize potential-parameters for solid systems, was developed based on real-coded genetic algorithm (GA). Fitness (=optimization-function) in GA for potential-parameter optimization could be calculated in practical time, and a concept of the corresponded module in GA-code was proposed. The developed software has an extensible structure: a user can define a new crystal-structure, or a new potential function to use in potential-parameter optimization by defining a corresponded class for that in separated header files. Convenient interfacial class to calculate equilibrium material properties of crystals and that to calculate material properties of user-inputted atomic-structures were prepared to define optimization-function. Several sample input files and header files were available for easy starting. As a result of distribution, several effective interatomic potentials were developed by using the software. As a sample of the development of interatomic potential, Tersoff-type potential for SiO2 systems were shown.