Quench Molecular Dynamics Research Articles

A close-packed sphere model for characterising porous networks in atomistic simulations and its application in energy storage and conversion

Hierarchical (micro, meso & macro) porosity in materials plays a crucial role in influencing the movement of ions which governs the energy and power density during energy storage and conversion. The extant available methods to characterise porosity across scales (nano to meso to macro) lacks rigour and accuracy. Having accurate assessment of the porosity in materials can unlock new designs of electrodes for energy efficient energy storage and conversion devices such as batteries, supercapacitors and fuel cells. Through this work, we report the systematic development of a method to fully characterise the carbon porous networks using a molecular dynamics simulation testbed. Our work entails modelling and simulation of porous carbon structures using quenched molecular dynamics (QMD) simulations using Gaussian Approximation potential (GAP) and benchmarking the results with prior literature. This modelling technique can reliably be used for quantitative characterisation of the interconnectivity in porous structures to study ionic movements and charge transfer mechanisms. A new parameter, namely nearest neighbour search (NNS) coefficient was introduced to quantify homogeneity and networking in the porous structures. NNS coefficient increased from 1.62 to 1.92 with decrease of the annealing temperature from 8000 K to 4000 K in carbon. The procedure outlined was although tested on porous carbon networks, but adaptable to study any other material system at multi-length scales.

Characterization of quenched MD simulated porous carbon electrodes for supercapacitors

Energy storage devices are playing a significant role in reducing the harmful effects of global warming. Automobile manufacturers are already shifting towards electric vehicles (EVs) in order to curb vehicular pollution. One of the significant drawbacks of the current EV batteries lies in their power density which limits their application. Supercapacitors are a category of energy storage devices that keep excellent specific power capacity and can be used in a hybrid setup with Li-ion batteries in order to make EVs with longer life and rapid acceleration. Electrode porosity in supercapacitors performs a major role in defining their energy and power density. This work explores the quenched molecular dynamics (QMD) simulations followed by thorough characterization for understanding the bimodal pore size distribution (combination of micro- & mesopores) of a porous electrode structure for maintaining a high energy and power density. We performed simulations at various quench rates on porous carbon structures ranging from 600 K/ps to 5 K/ps. Once the porous structures obtained room temperature (300 K), we characterized it for its pore sizes that allow ions to move in and out of the pores during charging and discharging, respectively. The interconnected channeling method has been developed to identify the channel throats and their lengths for different cases of quench rates. Direct output of this study will help experimentalists in fabricating tunable porosity in order to achieve high energy density while maintaining a relatively good power density of supercapacitors.

Designing porous electrode structures for supercapacitors using quenched MD simulations

Recently, supercapacitors with hierarchical porous structured electrodes are gaining a lot of research interest due to their unique qualities such as high power, durability and eco-friendly nature. In this study, porous structured electrodes were generated using quenched molecular dynamics (QMD) simulations, that can provide high energy density by virtue of high porosity. Here, three different quench rates (16, 8 and 4 K/ps) were applied on liquid carbon system to generate different porous structures. It was observed that at 4000 K, the carbon atoms become disorderly bonded and arranges themselves in an ordered hexagonal ring sheets after the completion of quenching process at 300 K. The porous carbon structures were visualized by contour surface mesh. The pore size distribution showed an increase of 62% on decreasing the quench rate from 16 K/ps to 4 K/ps. These light-weight porous carbon structures may also be tested for mechanical and electrical performances, which can have future implications as electrodes for supercapacitor.

Wavelet neural network modeling for the retention efficiency of sub-15 nm nanoparticles in ultrafiltration under small particle to pore diameter ratio

Ultrafiltration (UF) using membranes with a small ratio of particle to pore diameter (PPD) would be very desirable for energy saving. The nanoparticle (NP) retention efficiency of membranes with a small PPD ratio depends on various physical and chemical properties of NPs, membranes and solutions as well as the filtration conditions. Until now, no simple model is available for the calculation of NP retention efficiency in UF membranes, besides, it is unlikely to conduct experiments covering all conditions for obtaining the efficiency. The artificial neural network (ANN) has been attracting much attention for studying the performance of a highly nonlinear system. In this study, a wavelet ANN model was developed to predict the NP retentions in membranes for the dead-ended UFs under different conditions. A total of 13 parameters, including the membrane features, particle properties, water solution characteristics, operating conditions, etc., are considered as ANN inputs and the NP retention efficiency as the output. A total of 200 datasets with high quality from literature were selected, in which 50% were for the model training, 30% for the model validation and the remaining 20% for the model testing. A high correlation between the output and inputs was obtained and the significance of the 13 parameters on the NP retention was ranked. A case study was performed to further validate the trained ANN model in the prediction of the retention efficiency of 10 nm gold NPs in a 50 nm pore sized polycarbonate track etched (PCTE) membrane at different pH conditions (5–9). Focusing on the variation of pH, an excellent agreement between the model prediction and the calculation by the modified extended Derjaguin Landau Verwey Overbeek-Maxwell (MEDLVO-Maxwell) model originating from classical and extended DLVO theory was obtained. The interaction energy in the MEDLVO-Maxwell model was based on the separation distance calculated by a quench molecular dynamics (MD) simulation. This study illustrates and validates the application of ANN modeling on the NP retention efficiency prediction in the UF with small PPD ratios.

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS).

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, "minimalist helical mimics". It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i + 4, i + 7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i + 3, i + 7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; (iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain "triads" in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the "side-chain correspondences" (e.g. i, i + 4, i + 7 or i, i + 3, i + 4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1-8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites.

Atomistic models for disordered nanoporous carbons using reactive force fields

Optimization of disordered nanoporous carbons (DNCs) for specific applications remains a challenge due to the difficulty in accurately characterizing their nanostructures with current experimental methods. We describe how atomistic simulation techniques can be used to build structural models of DNCs and subsequently elucidate the structure–function relationship in these complex porous materials. In particular, two state-of-the-art approaches that use methods based in statistical mechanics to predict the structure of DNCs are described. The quench molecular dynamics method is a pseudo-mimetic approach that captures the effect of synthesis temperature on the structural morphology of disordered carbons, while the hybrid reverse Monte Carlo method is a reconstruction approach that builds realistic replicas of DNCs from experimental diffraction data. Both of these methods use reactive force fields to capture the formation and disassociation of chemical bonds during the simulations, allowing for the structural and porous features of DNCs to be predicted. We describe the principles behind these methods and provide illustrative examples that demonstrate their utility in modeling DNCs. Finally, we also discuss their current limitations and future avenues for improving their predictive capabilities.

Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations

Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.

Self-diffusion behaviors of Pd adatom and dimer on Pd(001) surface

Abstract Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of Pd adatom and dimer on Pd(0 0 1) surface have been studied in the temperature ranges from 600 K to 900 K. The simulation time varies from 25 to 50 ns according to the different substrate temperature. The diffusion mechanism of both the single Pd adatom and dimer is the simple exchange mechanism with the substrate atoms. The diffusion prefactors D 0 and activation energies E a are derived from the Arrhenius relation. The activation energy E a is in good agreement with the result of the quench molecular dynamics and experimental data of the single Pd adatom. The activation energy 0.58 ± 0.02 eV of the dimer is slightly lower than that 0.63 ± 0.02 eV of the single adatom because of the higher coordination numbers. When substrate temperature T = 290 K, the diffusion mobility D of the single adatom is equal to that of the dimer. In addition, the remarkable self-diffusion behaviors in several previous experiments that the diffusion mobility of the dimer is higher than that of the single adatom at low temperature are explained according to our molecular dynamics results.

Tilted and nontilted Ag overlayer on a Ni(111) substrate: Structure and energetics

The first stages of silver growth on a nickel (111) surface, for coverages up to 2 monolayers, have been investigated by quenched molecular dynamics (QMD) simulations and low energy electron diffraction (LEED). After a thermal treatment, a collinear $(7\ifmmode\times\else\texttimes\fi{}7)$ reconstruction, with $\text{Ag}(111)\ensuremath{\parallel}\text{Ni}(111)$ and $\text{Ag}[1\overline{1}0]\ensuremath{\parallel}\text{Ni}[1\overline{1}0]$, observed at room temperature, is seen to change into a tilted reconstruction where the silver lattice is rotated by $2.4\ifmmode\pm\else\textpm\fi{}0.4\ifmmode^\circ\else\textdegree\fi{}$ with respect to the substrate, the new cell dimensions being close to the $(7\ifmmode\times\else\texttimes\fi{}7)$ ones. In order to determine the geometry of this kind of tilted but still commensurate reconstruction, we have generated a large number of solutions with a rotation of the silver layer from $1\ifmmode^\circ\else\textdegree\fi{}$ to $40\ifmmode^\circ\else\textdegree\fi{}$ with respect to the substrate. The adsorption energies calculated by QMD simulations have shown that three of those tilted reconstructions, corresponding, respectively, to rotation angles equal to $1\ifmmode^\circ\else\textdegree\fi{}$, $2.2\ifmmode^\circ\else\textdegree\fi{}$, and $3.5\ifmmode^\circ\else\textdegree\fi{}$, are energetically more stable than the collinear one. These results support not only the present LEED data but also the tilted superstructures observed by various authors using LEED or scanning tunneling microscopy.

Elastic Properties of Mimetically Synthesized Model Nanoporous Carbon

AbstractActivated carbon is widely used for its attractive diffusion, adsorption and reaction properties. However, its mechanical behavior has received much less attention. We present a molecular dynamics simulation study on the elastic properties of activated carbon with nanometer-sized pores. The nanoporous carbon sample is composed of curved and defected graphene sheets, which is synthesized using quench molecular dynamics (QMD) method [1]. One unique feature of the current model is the mechanical stability, thus the bulk modulus, Young’s modulus, shear modulus and Poisson’s ratio can be obtained from simulated mechanical tests. By varying the density of the nanoporous carbon model, it was further found that the bulk modulus vs. density relation follows Gibson-Ashby type power law with exponents of 2.80 at low densities and 1.65 at high densities.

A mimetic porous carbon model by quench molecular dynamics simulation

A mimetic porous carbon model is generated using quench molecular dynamics simulations that reproduces experimental radial distribution functions of activated carbon. The resulting structure is composed of curved and defected graphene sheets. The curvature is induced by nonhexagonal rings. The quench conditions are systematically varied and the final porous structure is scrutinized in terms of its pore size distribution, pore connectivity, and fractal dimension. It is found that the initial carbon density affects the fractal dimension but only causes a minor shift in the pore size distribution. On the other hand, the quench rate affects the pore size distribution but only causes a minor shift in the fractal dimension.

Thermodynamic considerations and computer simulations on the formation of core-shell nanoparticles under electrochemical conditions

We report on thermodynamic modeling and computer simulations on the electrochemical generation of metallic and bimetallic nanoparticles (NPs) by means of quenched molecular dynamics (QMD). The present results suggest that the spontaneous formation of core-shell NPs depends on several factors, i.e. size and shape of the core, chemical composition of the system, and under-/oversaturation conditions. Homo- and heteroatomic prototypical systems were considered. The former systems were Au and Pt. The latter were Ag(core)/Au(shell), Pt(core)/Au(shell), Au(core)/Ag(shell) and Au(core)/Pt(shell).

Synthesis and conformational preferences of unnatural tetrapeptides containing l-valine units

The stereoselective synthesis of non-proteinogenic tetrapeptides 7, 16 and 17 containing two l-valine units and two modified α-amino acids (proline and aspartic acid) has been accomplished starting from the l-valine derived chiral synthon 1. Investigations of the conformational preference and structure of these unnatural peptides were carried out using 1H NMR and IR spectroscopic techniques and a conformational analysis based on quenched molecular dynamics (QMD).

A quenched molecular dynamics-rotating frame Overhauser spectroscopy study of a series of semibiosynthetically monoacylated anthocyanins.

Quenched molecular dynamics (QMD), in conjunction with NMR (ROESY) studies, was used to investigate the conformational behavior of some semibiosynthetic anthocyanins of the type 6-O-acyl-beta-D-Glcp-(166)-beta-D-Galp-(1-->O(3))-cyanidin, with and without a beta-D-Xylp branch at the 2-O-Gal position. These compounds, which are produced by the addition of selected carboxylic acids to growing tissue cultures of Daucus carota (wild carrot), are of interest as color-stabilized anthocyanins, some of which have potential as useful colorants in the nutraceutical and pharmaceutical industries. The QMD-ROESY studies, performed for the first time on anthocyanins, have led to the identification of families of conformers of these flexible molecules that are of interest in work toward determining the mechanism for stabilization of color among these compounds in solution.

Pore Size Distribution of Porous Glasses: A Test of the Independent Pore Model

Using the Kierlik and Rosinberg fundamental measure theory, we test the density functional theory method for determination of pore size distributions from adsorption data for porous glasses. The glasses chosen for study are model glasses prepared by a quench molecular dynamics method that mimics the experimental synthesis process and are completely characterized at the molecular level. The density functional method involves two approximations: (a) the glasses can be regarded as made up of a distribution of nonconnected pores of simple geometry, which we refer to as the independent pore model, and (b) the adsorption isotherms for these nonconnected pores can be described by the density functional theory. Using simulated adsorption isotherm data for the glasses and adsorption isotherms for the pores of simple geometry calculated by the density functional theory, a regularization method is used to determine the pore size distribution from the adsorption data. These calculated pore size distributions, as well as the adsorption isotherms for the materials, are compared with the exact geometric pore size distributions for the material and with the simulated isotherms. Both slit-shaped and cylindrical pores are used in the density functional theory method. It is found that a unique geometry is not able to accurately describe the whole adsorption isotherm. The use of slit-shaped pores gives overall better results, although the low-pressure regime is more accurate when cylindrical pores are used; reasons for this are discussed. The pore size distributions from the density functional theory are in reasonable agreement with the geometrical ones, giving the same shape and mean pore width and similar porosities in the four materials. Since it is known that the density functional theory gives excellent results for the adsorption isotherms (approximation b above), this comparison tests the independent pore model directly.

Folded conformation of an immunostimulating tetrapeptide Rigin: high temperature molecular dynamics simulation study

Employing high temperature quenched molecular dynamics (QMD) simulations the conformational energy space of an immunostimulating tetrapeptide rigin: H-Gly 341-Gln-Pro-Arg 344-OH, is explored. Using distance dependent dielectric (ε= r ij ) 31 different low energy starting structures with identical sequence were computed for their conformational preferences. According to the hypothesis of O'Connors et al. [ J. Med. Chem. 35 (1992), 2870], 83 low-energy conformers resulted from unrestrained molecular dynamics (MD) simulations, could be classified into two energy minimized families: A and B, comprised of 64 (Pro C γ- endo orientation) and 19 (Pro C γ- exo orientation) structures, respectively. An examination of these families revealed the existence of a remarkably similar folded backbone conformation: torsion angles being φ i+1 ≈−65°, ψ i+1 ≈−65°, φ i+2 ≈−65°, ψ i+2 ≈−60°, characterizing a distorted type III β-turn structure across the central Gln-Pro segment. The folded conformation of rigin is devoid of a classical 1 ← 4 intra-molecular hydrogen bond nevertheless, the conformation is stabilized by an effective ‘ salt-bridge’, i.e., Gly H 3N +… C αOO − Arg interaction. Surprisingly, in both the families the unusual folded side-chain dispositions of the Gln residue favor the formation of a unique intra-residue ‘main-chain to side-chain’ H-bond, i.e., N α–H…N ϵ interaction, encompassing a seven-membered ring motif. The conformational attributes may be valuable in de novo construction of structure-based drug candidates having sufficient stimulating activity.

Characterization of Porous Glasses: Simulation Models, Adsorption Isotherms, and the Brunauer−Emmett−Teller Analysis Method

We have developed a realistic model for studying adsorption in porous glasses which reproduces the complex structure of these materials. The model porous material is generated by a quench molecular dynamics procedure which mimics the processes by which Vycor glass and controlled-pore glasses are produced. We examine this procedure and the resulting model materials by a variety of methods and find that they have porosities, pore sizes, and surface areas very similar to the real glasses. These simulated glasses have precisely known properties (surface area, pore size distribution, etc.), in contrast to experimental glasses; computer experiments on such model glasses can therefore be used to test new and existing experimental methods of characterization. We calculate the adsorption isotherms for a model of nitrogen adsorbing onto these materials and analyze these data using the BET isotherm. The BET monolayer density exhibits systematic variations with both the average pore size and the porosity of the model...

Liquid-liquid phase separation in cylindrical pores: Quench molecular dynamics and Monte Carlo simulations

We have studied the liquid-liquid phase separation of a binary mixture confined in three different cylindrical pores by several simulation methods. The phase diagrams of the fluid mixture in the three pores were determined using histogram-biased semigrand Monte Carlo simulations, and the kinetics of phase separation of the confined liquid mixture were studied using quench molecular dynamics. In these systems, the interactions between the two fluids and the pore wall are identical so that no wetting occurs and the fluid separates into a series of pluglike domains after a temperature quench. We have determined that the growth of these domains is given by a power law for systems near to their critical temperature, while for deeper quenches it proceeds by a power law at short times which crosses over to a slower growth when the plug-shaped domains are large enough to completely block the pore. Domains in these systems are shown to grow by a condensation mechanism. Using a simple thermodynamic model we analyze the $P(X)$ probability distributions from our Monte Carlo simulations, and estimate the equilibrium domain lengths in two pores over a range of temperature. These lengths are larger than those reached in our molecular dynamics simulations. In order to assess these estimations, we have performed very long canonical Monte Carlo simulations to directly determine the equilibrium domain lengths in a few of these pores.

Conformations of cis- and trans-2,3-methanomethionine stereoisomers in the tripeptide mimic system Ac[cyclo-M]NHiPr.

Quenched molecular dynamics (QMD) was used to simulate low-energy conformers of the tripeptide mimics Ac¿cyclo-Met¿NHiPr, where the 2.3-methanomethionine is the cis-derivative (2R,3S)-cyclo-Met and the trans-derivative (2R,3R)-cyclo-Met. Variations of the favored omicron, upsilon values. and differences between the simulated preferred conformations for the two structures, were rationalized and discussed. Physical data for the cis-derivative (NMR, CD and FT-IR) gave no conclusive evidence for any preferred conformation. However for the trans-derivative, Ac¿(2R,3R)-cyclo-Met¿NHiPr, the physical data suggests that a conformer with partial helical structure is favored. This work provides details of how the rigidly constrained side chain and cyclopropane of 2,3-methanoamino acids can be used to manipulate phi, psi values in a logical fashion.

Multilayer relaxation and reconstruction in bcc and fcc transition and noble metals

Using a tight-binding scheme and a ‘quenched-molecular dynamics’ method, we calculate the multilayer relaxation of bcc transition metals for the (110), (100) and (111) faces (which present only perpendicular relaxations) and the (211), (310) and (210) faces (for which both parallel and perpendicular components are present). Moreover, we account for the multilayer reconstruction of W(100) and its non-occurrence for Ta(100). Then performing similar calculations in the case of all fcc transition and noble metals, we obtain the multilayer relaxation of the low index surfaces: (111), (100) and (110). Finally, we explain the material dependence of the (1 × 2) reconstruction of the (110) face, which is only observed for the 5d metals (Ir, Pt, Au). The model allows us to predict order-disorder surface phase transition for the (110) face of all these fcc metals.