Principles Molecular Dynamics Simulations Research Articles

Two-dimensional material nanopores as biosensors: Recent progress based on computations and simulations

The passage of molecules through nanoscale pores is ubiquitous in biology. Inspired by this process, nanopore-based biosensors were proposed and have been widely used to probe, analyze or manipulate single biomolecules, such as DNA, RNA and protein. In a typical nanopore experiment, a thin membrane containing a nanoscale pore is used to separate two chambers of conducting electrolyte solution. As a transmembrane voltage bias is applied, analytes (such as DNA and RNA) in solution are driven through the nanopore, leading to changes in recorded ionic current traces. These changes are related to physical or chemical properties of the translocating molecules (analytes) such as structure, configuration and even identity. When DNA molecules are used as the analytes, the ionic current signal could be used to recognize individual bases, and in turn, the DNA sequence. The advantage of nanopore method for sequencing applications lies in its low cost, high efficiency, and ultra-long reads, because it eliminates the need for sample amplification and fluorescence labeling steps. In 1996, Kasianowicz et al. reported the first experiment of single-stranded DNA and RNA molecules passing through the biological pore α -hemolysin. In the following years, many other biological nanopores were used in order to obtain sufficient current and temporal resolution for single-molecule analysis. For example, the MspA nanopore, incorporated with Phi29 DNA polymerase, is able to read the sequence information of a single-stranded DNA (ssDNA) through measured ionic current. The relatively sharp and short constriction of the MspA nanopore compared to other biological nanopores (e.g., α -hemolysin) is regarded as the structural origin for its outstanding sensing ability. In particular, the length of the constriction in the MspA nanopore is equivalent to the distance between neighboring DNA bases in an ssDNA strand. This observation implied that a monolayer of typical two-dimensional (2D) materials such as graphene, with a thickness also equivalent to the spatial interval of DNA bases, is a promising candidate for DNA sequencing. On one hand, 2D material nanopores share inherent advantages of traditional solid-state nanopores, such as high stability over a broad range of temperature, pH and applied electric fields. On the other hand, the extreme thinness of 2D material nanopores is expected to deliver much higher spatial resolution than nanopores in traditional solid-state membranes such as silicon nitride and silicon oxide, which typically contain hundreds of bases in the pores simultaneously. Furthermore, the use of electrically conducting 2D materials offers the possibility to detect analytes at higher bandwidths, namely, by measuring transverse in-plane current through 2D material nanoribbons. During the development of nanopores sensors, computational tools such as first principle calculations and molecular dynamics simulations that can resolve molecular-scale interactions in nanopores have made significant contributions to this area in terms of prediction of novel detection approaches, optimization of device performance and explanation of experimental phenomena, etc. Here, with a standing point of computations and simulations, this review surveys the milestones in the area of 2D material nanopore-based biosensors, and the key experimental progress is also briefly discussed. Not limited to ionic current measurement, several other measurement methods such as transverse current in a nanoribbon and force traces during the pulling of biomolecules through nanopores are also introduced. This review further outlines key factors that restrict the performance of these sensors and discusses challenges and possible solutions. The key challenges include fast biomolecular translocation across nanopores and high noise levels in the recorded signal, etc. Finally, we provide a discussion on the future direction for the field, including the rational choice of 2D material, precise control over molecular movement inside nanopores as well as exploration of new applications.

Negligible Effect on the Structure and Vibrational Spectral Dynamics of Water Molecules Near Hydrophobic Solutes

AbstractThe first principles molecular dynamics simulations were performed to study the structural, dynamical, and spectral properties of water molecules in the vicinity of hydrophobic molecules. A layer‐wise distance‐dependent angular distribution calculation was performed to understand the effects of neopentane (NEO) and tert‐butyl alcohol (TBA) on the orientation profile of water molecules. We found no evidence of an increasing tetrahedral structure of water molecules inside the first solvation shell of NEO and TBA; this indicates the presence of less ordered water molecules inside the solvation shell. The water molecules, however, retained their bulk‐like property by accruing three to four hydrogen bonds per water molecule in bulk. The long‐lived non‐hydrogen‐bonded or dangling OH bonds were observed in the hydration shells of both the molecules as compared to the bulk water, where such dangling OH bonds were less. The high peak frequency of dangling OH oscillators in the hydration shell was found to be similar to the previously obtained dangling OH chromophores in experimental and theoretical studies. We also report the rotational dynamics of water molecules. Our calculations suggest that the slowing down of water molecules near the hydrophobic solutes is moderate as compared to that of bulk water due to the lack of hydrogen bond exchangeable partners. Therefore, our results are in complete contrast with the idea of the iceberg of Frank and Evan.

Powerful predictability of FPMD simulations for the phase transition behavior of NaCl-MgCl2 eutectic salt

First principle molecular dynamics (FPMD) simulations in combination with experimental measurements are applied to investigate the phase transition behavior of NaCl-MgCl2 eutectic salt from 823 to 573 K. First, the essential phase transition indexes of thermal expansion coefficient, density, melting point, and enthalpy of fusion for NaCl-MgCl2 eutectic obtained by simulations and experiments are in good agreement with each other. Second, the micro-structural characteristics during phase transition are depicted by the temperature dependences of angular distribution function, radial distribution function and coordination number. The structural evolution of NaCl-MgCl2 eutectic is illustrated from the rearrangement of polyhedral MgCln2-n clusters, and it is founded that high and low temperature are conducive to the formation of 4-fold and 6-fold coordinated structure, respectively. Third, the ionic self-diffusion coefficients for NaCl-MgCl2 eutectic are predicted and concluded that Mg2+ behaves like a complex than as a free ion resulting in less diffusivity. Therefore, the shear viscosities of molten NaCl-MgCl2 as well as the corresponding pre-exponential factor and activation energy are evaluated considering the solvodynamic mean radius of all the diffusive particles. Ultimately, two figures of merit for molten NaCl-MgCl2 are deduced to evaluate the heat-transfer and heat-loss performance by integrating multiple thermal properties including density, viscosity, specific heat capacity and thermal conductivity. Overall, these simulation results are in satisfactory agreement with available reference data, indicating that the FPMD simulations work extremely well in predicting the thermophysical and structural properties of NaCl-MgCl2, which also provide insights for the applications of binary chloride salts in thermal energy storage.

Differing preferential ion binding to the peptide bond in ionic environment from classical and first principles molecular dynamics simulations

The interactions of ions with N-methylacetamide (NMA) in hydrated ionic liquid (IL), methylammonium formate (MAF), with varying concentrations were studied by molecular dynamics simulations. As the interactions depend on the choice of potential, the current study aims to compare the preferential binding of cation and anion of MAF to peptide bond of NMA utilizing force field-based classical molecular dynamics (CMD) and first principles molecular dynamics (FPMD) simulations. NMA forms a stable hydrogen bonding network with anion. First principles molecular dynamics simulations predict hydrogen bonding interaction with both anion and cation in pure IL. In contrast, the classical molecular dynamics simulations provide evidence of the strong interaction of NMA with anion only. However, NMA interacts with cation in the presence of water as a co-solvent. Water molecules facilitate the more significant cation-anion distance, which decreases the electrostatic interaction between ions. In aqueous solutions, the self-diffusivity of the entities increases as compared to pure IL. The value of residence time rises with an increase in the concentration of IL. The analysis of hydrogen bond auto-correlation function reveals that with increasing IL concentration, the short-range force increases, and simultaneously, the lifetime of intermolecular hydrogen bonds increases. Between NMA-cation and NMA-anion, the strength of the NMA-anion hydrogen bond is stronger than the former. The preferential solvation is due to nature of predefined classical potential as compared to FPMD simulations.

Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water

We report the vibrational dynamics of amide modes of N-methylformamide (NMF), N-methylacetamide (NMA), and N, N-dimethylacetamide (DMA) in water using first principles molecular dynamics simulations. The solvent-mediated dynamics and stretching profile of CO, NH, and CN modes of amide molecules were analyzed in terms of vibrational spectral and second-order reorientational dynamical properties. The maximum redshift is observed for the amide I band of DMA due to stronger DMA-water hydrogen bonding interaction; a blue shift is observed for NMF. The calculations also reveal that the amide-A band of NMF exhibits a redshift as compared to NMA. Multiple peaks are located for the CN band of DMA, and this feature gradually decreases for NMA and NMF. Spectral dynamics of amide bands were investigated by calculating the frequency-frequency correlation functions. Slowest spectral diffusion is found for the CO band of DMA. However, NMA shows slower dynamics for NH band than that of NMF.

Coordination of Zr4+/Hf4+/Nb5+/Ta5+ in silicate melts: insight from first principles molecular dynamics simulations

The highly fractionated granites related to the ore deposits of strategic critical metals such as Zr, Hf, Nb and Ta are usually rich in fluorine, but how fluorine influences the magmatic ore-forming processes of these metals is still unclear. Zr4+/Hf4+/Nb5+/Ta5+—F− complexation in silicate melts cannot be identified with the current experimental methods. In this study, by using first principles molecular dynamics (FPMD) technique, we investigated the structures of Zr4+, Hf4+, Nb5+, Ta5+ and F− in albite melts to reveal their coordination geochemistry in highly fractionated granitic magmas. We obtained 6-fold Zr4+/Hf4+/Nb5+/Ta5+—O2− coordinations with the average bond lengths of about 2.0 Å and 1.9 Å for Zr4+/Hf4+—O2− and Nb5+/Ta5+—O2− respectively in both anhydrous and hydrous melts, and found that there was no Zr4+/Hf4+/Nb5+/Ta5+—F− complexation. F− bound with Si and Al in silicate melts, which generated non-bridging oxygens (NBO). With these findings, it is concluded that there is no direct chemical interaction between F− and Zr4+/Hf4+/Nb5+/Ta5+ in silicate melts and fluorine influences their ore-forming processes through indirect effects.

Metallic VS2/blue phosphorene heterostructures as promising anode materials for high-performance lithium ion batteries: A first principles study

In this work, based on first principles calculations and molecular dynamics simulation, we systematically investigated the VS2/blue phosphorene (BlueP) heterostructures as potential anodes for LIBs. Our results show that both H-VS2/BlueP and T-VS2/BlueP heterostructures exhibit metallic characteristics, ensuring good electrical conductivity for the fast electron transport. The Young’s moduli (187.3 N/m for H-VS2/BlueP and 183.4 N/m for T-VS2/BlueP), mechanical flexibility (ultimate strains > 16%) and adsorption energy of VS2/BlueP heterostructures are remarkably improved in comparison with pristine BlueP. Such improved mechanical property and adsorption energy are of great significance to suppress the anode pulverization on the whole lithium intercalation–deintercalation process. Moreover, the specific capacities of VS2/BlueP heterostructures are up to 1211.34 mA h/g (multi-layer Li adsorption), which are much higher than pristine BlueP and commercial graphite anodes. In addition, diffusion barriers in the H-VS2/BlueP and T-VS2/BlueP heterostructures are 0.17, 0.16 eV, respectively, implying high mobility of Li. All these encouraging results indicate that VS2/BlueP heterostructures are promising anodes to achieve advanced LIBs.

Insight into dynamic interaction of molten MgCl2-NaCl-KCl with impurity water via FPMD simulations

First principle molecular dynamics (FPMD) simulations are used to investigate the dynamic interaction of impurity water with molten MgCl2-NaCl-KCl which has emerged as one of attractive candidate salts for the generation III concentrated solar power plant. The energetic fluctuations, radial distribution functions, micro-morphologies of intermediates, vibrational characteristics, and ionic self-diffusion coefficients of hydrous MgCl2-NaCl-KCl (hMNK) systems at 773 K are demonstrated, respectively. It is concluded that the O2− will eventually tend to interact with Mg2+ regardless of the initial water distribution. Besides, the evolution of Mg–O interatomic distance over time is depicted, from which the shuttles of O2− in the coordination shell of Mg-centered polyhedrons are captured. Furthermore, the simulated stretching vibration spectra of Mg–O and H–O bonds are comparable with experimental results, suggesting the powerful predictivity of FPMD. Overall, the water in molten hMNK promotes the migration of K+ rather than Na+, and the ionic transport properties depend on the water content and spatial distribution. And these FPMD results are heuristic in understanding the structure-activity relationship of molten hMNK, which sheds insight for the development of salt purification technology.

Strong Differential Monovalent Anion Selectivity in Narrow Diameter Carbon Nanotube Porins

Inner pores of carbon nanotubes combine extremely fast water transport and ion selectivity that could potentially be useful for high-performance water desalination and separation applications. We used dye-quenching halide assays and stopped-flow spectrometry to determine intrinsic permeability of three small monovalent halide anions (chloride, bromide, iodide) and one pseudohalide anion (thiocyanate) through narrow 0.8 nm diameter carbon nanotube porins (CNTPs). These measurements revealed unexpectedly strong differential ion selectivity with permeabilities of different ions varying by up to 2 orders of magnitude. Removal of the negative charge from the nanotube entrance increased anion permeability by only a relatively small factor, indicating that electrostatic repulsion was not a major determinant of CNTP selectivity. First principle molecular dynamics simulations revealed that the origin of this strong differential ion selectivity is partial dehydration of anions upon entry into the narrow CNTP channels.

Unrevealing the thermophysical properties and microstructural evolution of MgCl2–NaCl–KCl eutectic: FPMD simulations and experimental measurements

The first principle molecular dynamics (FPMD) simulations in combination with experimental measurements are applied to investigate the thermophysical properties and structural evolution of MgCl2–NaCl–KCl (MNK) eutectic. The densities, melting point, and enthalpy of fusion simulated by FPMD within NPT ensemble are consistent with experimental results. Besides, the thermal conductivity of molten MNK eutectic evaluated from FPMD simulations with NVT ensemble gives satisfactory result. Furthermore, the shear viscosities of MNK eutectic are deduced based on ion self-diffusion coefficients and solvodynamic radius, similar to the data estimated by additive contribution method. Eventually, the change rules of radial and angular distribution functions and structural factor of MNK eutectic during melting are revealed, and the melting mechanism is proposed from the evolution of polyhedral coordination structures. These results are heuristic in structure-activity relationship of MNK eutectic, which sheds insight for further development of efficient heat transfer and storage media through microstructure engineering.

A two-dimensional liquid-like phase on Ga-rich GaN (0001) surfaces evidenced by first principles molecular dynamics

First principles molecular dynamics simulations have been used as a tool to investigate at an atomistic level the finite temperature behavior of a typical GaN growing surface. At 1300 K, Ga adatoms show a high degree of destabilization and a departure of the diffusivity from an ordinary Arrhenius trend. Two signatures, a drastic change in the radial distribution function and a sudden increase of the diffusion constant, allow to quantify such a diffusion process. Such a high diffusivity results in the arising of a pronounced peak at about 2.6 Å, typical of Ga–Ga bonds, indicating a tendency to cluster together of the Ga adatoms. Along with the remarkable diffusivity observed at 1300 K, this result indicates rather clearly that at the typical experimental temperature, the epitaxial growth occurs not on a rigid surface in which Ga adatoms are tightly bound to specific sites, but rather on a two-dimensional liquid state.

Conformational dynamics of aqueous hydrogen peroxide from first principles molecular dynamics simulations.

We performed first principles molecular dynamics simulations of a relatively dilute aqueous hydrogen peroxide (H2O2) solution to examine its structural alterations and relevant dynamics upon solvation. The internal rotation of the OH groups about the O-O bond facilitates the flexible structure of H2O2. Structural calculations reveal dihedral angle fluctuations in the aqueous solution. Water molecules make stronger hydrogen bonds through the hydrogen atom of the solute than the oxygen atom leading to distinct hydrogen bonding configurations inside the first solvation shell. Time-dependent dihedral angle alterations result in conformational changes and the normalized dihedral angle distribution plot displays characteristic peaks at ∼100-120° and ∼230°, illustrating various conformational states. Within the simulation time, flexibility-induced interconversion of hydrogen peroxide gives rise to several cisoid and transoid conformers. In this study, we examine the relative population of the associated conformational states and the lifetime of the cisoid and transoid conformers from the torsion angle variations. We also determine the free energy landscape of the rotational isomerization process in H2O2 and explore two distinct energy barriers during such interconversion.

Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives

First principles molecular dynamics (FPMD) simulations of relatively dilute aqueous solutions of N-methylformamide (NMF), N, N-dimethylacetamide (DMA), N-methylacetamide (NMA) were carried out to elucidate the effects of variation of hydrophobicity of amide molecules on structure, dynamics and spectral properties of solvating water molecules. A quantitative analysis of dangling OH groups of water molecules, one of the consequences of hydrophobicity, around the amide molecules was performed to explore the structure of surrounding water molecules. We observe that DMA has the most hydrophobic character among the three amide molecules; the lifetime of dangling OH mode of water molecules and the number of such modes are found to be more inside the solvation shell of DMA as compared to NMA and NMF molecules. Overall this lifetime is more inside the solvation shell of amides compared to the bulk water molecules for all aqueous solutions of amides. Rotational dynamics calculation suggests significant retardation of OH bonds of water near the amide oxygen atom (O) due to the OwHw⋯O strong hydrogen bonds. A moderate slowdown of reorientational dynamics is also observed for OH modes that are close to the hydrophobic surface of DMA in its aqueous solution. Vibrational density of states (VDOS) and frequency distribution calculations point out the higher average stretching frequency (~3600–3850 cm−1) of free OH groups. Hydrogen bond lifetime calculations conceive that DMA, having three methyl groups, makes stronger hydrogen bonds through the CO moiety. Vibrational spectral diffusion of bulk water and solvation shell water molecules were also calculated in combination with wavelet transform and frequency-frequency autocorrelation functions. The CO group affected OH stretching frequency bands for aqueous solutions of NMF and NMA molecules are more pronounced than that of DMA. However, NH affected OH frequency bands are less pronounced for NMA and DMA due to the presence of more number of hydrophobic methyl groups. Going from NMF to DMA, the OH frequency bands inside the amide solvation shells shift towards the higher value due to the enhancement of hydrophobicity. The vibrational spectral diffusion of OH modes around CO and NH (N for DMA) groups, as well as for bulk water molecules, is also investigated. Three time scales were found for these calculations for all the cases. The fast time scales in the range ~50–100 fs are due to the amide-water intact hydrogen bonding, and two slower time scales in the range ~0.6–3.90 ps and ~10–20 ps were found. The time scales in the range of ~0.6 to 3.90 ps can be attributed to carbonyl-water and N-H-water hydrogen bonding, and the very long time scales are due to the escape dynamics water molecules from the solvation shell of CO and NH (N for DMA) groups.

Structure and reactivity of highly reduced titanium oxide surface layers on TiO2: A first-principles study.

Titanium oxide structures featuring highly reduced TiOx films on top of nearly stoichiometric TiO2 hold promise for applications ranging from photocatalysis to resistance switching devices. Here, we focus on titanium monoxide (TiO) layers on anatase TiO2 (001) and use first principles calculations to investigate their structure and properties as well as their interface with liquid water. We find that only a single TiO layer can grow epitaxially on anatase (001) and subsequent growth leads to the formation of TiO islands. The TiO layers decrease the work function and enhance the surface conductivity in comparison to pure anatase, two features that can improve the TiO2 performance in photocatalytic hydrogen evolution but are thermodynamically unstable relative to pure TiO2 in humid/aqueous environment. Furthermore, first principles molecular dynamics simulations of the TiO (001)-water and anatase (001)-water interfaces show that unlike the multilayer structure of interfacial water on the anatase surface, a very dense and tightly packed first water layer is present on the surface of TiO, which could represent the first stage of partial surface reoxidation.

Crystallization properties of arsenic doped GST alloys

We present the enhanced properties observed in the phase change memory alloy Ge2Sb2Te5 (GST) when doped with arsenic. Although arsenic is known as a toxic element, our observations show that significant improvement can be obtained in GST systems on thermal stability, transition temperature between amorphous and crystalline phases and switching behaviors when doping with arsenic. Though both the GST and arsenic doped GST are amorphous in the as-deposited state, only GST alloy turns to crystalline NaCl-type structure after annealing at 150 °C for 1 h. Results from the resistance versus temperature study show a systematic increase in the transition temperature and resistivity in the amorphous and crystalline states when the arsenic percentage in the GST alloy increases. The crystallization temperature (Tc) of (GST)0.85As0.15 is higher than the Tc observed in GST. Optical band gap (Eopt) values of the as-deposited films show a clear increasing trend; 0.6 eV for GST to 0.76 eV for (GST)0.85As0.15. The decreases in Eopt for the samples annealed at higher temperatures shows significant optical contrast between the as-deposited and annealed samples. Though all (GST)1−xAsx alloys show memory switching behaviors, threshold switching voltages (VT) of the studied alloys show an increasing trend with arsenic doping. For (GST)0.85As0.15, VT is about 5.2 V, which is higher than GST (4.0 V). Higher transition temperature and higher threshold switching values show arsenic doping in GST can enhance the memory device properties by improving the thermal stability and data readability. Understanding the doping effect on the GST is important to understand its crystallization properties. Structure properties of amorphous GST, Ge2Sb2−0.3As0.3Te5 and (GST)0.85As0.15 models were studied using first principles molecular dynamics simulations, compared their partial radial distribution functions, and q parameter order. Arsenic doping into GST features interesting structural and electronic effects revealed by the radial distribution functions, q order parameter and band gap value, in line with the experimental findings.

Understanding the interfacial interactions of bioinspired chitosan-calcite nanocomposites by first principles molecular dynamics simulations and experimental FT-IR spectroscopy

The interfacial structures and bonding mechanism of the adsorption of chitosan monomers (GlcN and GlcNAc) on calcite (104) surface are investigated using first principles molecular dynamics simulations. It is revealed that the strong coordination CaO bonds are formed between five-fold coordinated Ca atoms on calcite surface and O atoms of hydroxyl groups (OH) and acetyl groups of chitosan in the chitosan-calcite nanocomposites, improving the chemical compatibility between organic and inorganic phases at the interface in the natural occurring nacre. Although, the presence of interfacial hydrogen bonds is also confirmed by analyzing the valence electron density difference in terms of induced dipole, the evolution of the equilibrium adsorption geometry is found to be mainly governed interfacial CaO coordination bonds. The amide group (NH2) of chitosan binds with calcite at the interface mainly through the formation of weak hydrogen bond. The predicted interfacial electronic structure can be either conductive (GlcNAc) or insulating (GlcN). The frequencies of the characteristic peaks in the calculated total and partial vibrational densities of states of GlcN/calcite systems are found to be in agreement with the FT-IR spectrum of the experimentally prepared chitosan-calcite nanocomposites, crucially validating the modelling structures and computational methodology employed in current work. Theoretical results strongly indicate that the peculiar adsorption in FT-IR spectrum at 2500 cm−1 is related to the presence of free GlcN molecule due to the hydrolysis of chitosan in aqueous solution.

Insight into the Role of Water on the Methylation of Hexamethylbenzene in H‐SAPO‐34 from First Principle Molecular Dynamics Simulations

AbstractThe methylation of hexamethylbenzene with methanol is one of the key reactions in the methanol‐to‐olefins hydrocarbon pool reaction cycle taking place over the industrially relevant H‐SAPO‐34 zeolite. This methylation reaction can occur either via a concerted or via a stepwise mechanism, the latter being the preferred pathway at higher temperatures. Herein, we systematically investigate how a complex reaction environment with additional water molecules and higher concentrations of Brønsted acid sites in the zeolite impacts the reaction mechanism. To this end, first principle molecular dynamics simulations are performed using enhanced sampling methods to characterize the reactants and products in the catalyst pores and to construct the free energy profiles. The most prominent effect of the dynamic sampling of the reaction path is the stabilization of the product region where water is formed, which can either move freely in the pores of the zeolite or be stabilized through hydrogen bonding with the other protic molecules. These protic molecules also stabilize the deprotonated Brønsted acid site, created due to the formation of the heptamethylbenzenium cation, via a Grotthuss‐type mechanism. Our results provide fundamental insight in the experimental parameters that impact the methylation of hexamethylbenzene in H‐SAPO‐34, especially highlighting and rationalizing the crucial role of water in one of the main reactions of the aromatics‐based reaction cycle.

Differential penetration of ethanol and water in Si-chabazite: High pressure dehydration of azeotrope solution

Abstract This study is aimed to shed light on the mechanisms at the basis of the differential penetration of alcohol and water in hydrophobic zeolites at ambient (Pamb) and non-ambient pressure. Here we report the effects of the penetration of water and alcohol in an all-silica chabazite (Si-CHA) compressed with an ethanol/water azeotrope solution (ethanol: water = 95.63 : 4.37 by mass %). We collected in situ synchrotron X-ray Powder Diffraction (XRPD) data in order to monitor the structural modifications induced by the fluid penetration and to investigate the guest-guest and host-guest interactions. First principles molecular dynamics simulations allowed to complete the structural description at high pressure, providing an atomistic level description of the guest-guest hydrogen bond network. For a comprehensive understanding of the processes involving the Si-CHA + azeotrope interactions, both the zeolite and the alcohol/water solution were firstly investigated separately under pressure. The results obtained prove that both H2O and ethanol penetrate Si-CHA porosities even at Pamb. However, while in these conditions the H2O/ethanol ratio adsorbed inside Si-CHA is similar to that of the external azeotrope solution, under pressure the zeolite extra-framework content corresponds to a composition much richer in H2O than the azeotrope one. Hence, our results suggest that a dehydration effect occurred on the azeotrope solution, promoted by pressure. In addition, the experiment performed to test the elastic behavior of Si-CHA with a non-penetrating pressure transmitting medium interestingly indicates that Si-pure chabazite is the most compressible zeolite among those up to now studied in silicone oil.

The self-diffusion coefficients of liquid binary M-Si (M=Al, Fe, Mg and Au) alloy systems by first principles molecular dynamics simulation

Through first-principles molecular dynamics simulation, the self-diffusion coefficients of five elements in the four liquid binary M-Si (M=Al,Fe,Mg,Au) alloy systems are obtained under the same overheating temperature. Except for DFe, the self-diffusion coefficient of the other four elements vary significantly with concentration of Si (cSi). The mixing enthalpy between Si and M elements determines the slop of DSi vs cSi curves in Si-rich range. The dominant factor on DSi is the partial coordination number of NSiSi: the larger the NSiSi is, the smaller DSi becomes. The secondary factor on DSi is the medium-range order in liquid alloys: the stronger the medium-range order is, the smaller DSi will be. Complex behavior of coupling or decoupling of self-diffusion coefficients in these liquid binary alloys are observed.

First Principles Calculation of the Entropy of Liquid Aluminum.

The information required to specify a liquid structure equals, in suitable units, its thermodynamic entropy. Hence, an expansion of the entropy in terms of multi-particle correlation functions can be interpreted as a hierarchy of information measures. Utilizing first principles molecular dynamics simulations, we simulate the structure of liquid aluminum to obtain its density, pair and triplet correlation functions, allowing us to approximate the experimentally measured entropy and relate the excess entropy to the information content of the correlation functions. We discuss the accuracy and convergence of the method.