First-principles Molecular Simulations Research Articles

First-principles calculation of P-type Mg3Sb2 thermoelectric performance modification by Ge and Si doping

Mg3Sb2 has been considered a highly promising thermoelectric material for mid-temperature applications. Optimizing the properties of the material is crucial for accelerating its commercial use. In this work, first-principles molecular simulations of P-type Mg3Sb2 doped with the carbon group elements Ge and Si have been carried out. Results indicate that doping with Ge and Si enhances the thermodynamic stability and electrical conductivity of the material. This improvement is achieved by decreasing the bandgap, increasing the local and peak density of states, flattening the band structure, and elevating the relative mass of carriers. Additionally, doping with Ge and Si decreases the phonon velocity and Debye temperature, which weakens the thermal transport properties of the material. These findings suggest that Ge and Si doping is an effective method for improving the thermoelectric properties of the material. At the same doping concentration, the Si single-doped system possesses the smallest bandgap value with the highest peak density of states and forms an indirect bandgap, leading to the best electrical transport properties; the Ge single-doped system has the lowest phonon velocity and Debye temperature, which has the most significant effect in attenuating the thermal transport properties of the material; and the Ge–Si co-doped system has the highest relative mass of carriers, which is conducive to the enhancement of Seebeck coefficient. The results offer theoretical guidance for experimentally analyzing the effects of Ge and Si doping on the thermoelectric properties of Mg3Sb2.

Impact of lignin–carbohydrate complex (LCC) linkages on cellulose pyrolysis chemistry

The prevalence of covalent lignin–carbohydrate complex (LCC) bonds likely foster inter-moiety reaction pathways, marked by significant kinetic and thermochemical barriers in the intra-moiety cellulose decomposition within LCC.

Solvation Structure and UV–Visible Absorption Spectra of the Nitrate Anion at the Air–Ice Interface by First-Principles Molecular Simulations

Solvation Structure and UV–Visible Absorption Spectra of the Nitrate Anion at the Air–Ice Interface by First-Principles Molecular Simulations

Elucidating the temperature and density dependence of silver chloride hydration numbers in high-temperature water vapor: A first-principles molecular simulation study

Hydration numbers of metal complexes in low-density aqueous solutions are required for developing geochemical models for ore-forming metals and for designing supercritical desalination processes. In this study, we investigate the temperature and density dependence of the hydration numbers of silver chloride at 623 K, 673 K, and 713 K and densities of 10–100 kg/m3. Experimental estimates of the hydration number in the literature for AgCl at these conditions are inconclusive and possibly contradictory as to the temperature and density dependence. First-principles molecular simulation presents an attractive alternative to experimental measurements. Specifically, recent work shows that machine-learning-accelerated nested Monte Carlo simulations provide reliable estimates for the hydration numbers of CuCl at 623 K from 10 to 100 kg/m3. Using the same technique, we find a monotonic temperature dependence, with the hydration number decreasing slightly with increasing temperature. In addition, the simulation-predicted hydration numbers steadily increase with increasing density. These temperature and density trends are in agreement with certain experimental data sets. Therefore, this work demonstrates how first-principles Monte Carlo simulations assist in resolving discrepancies between experimental data sets. Our simulation results also correctly predict that the hydration number, and thus also the solubility, of AgCl is lower than that of CuCl under the same conditions. Furthermore, the bond length and angle formed between the water complex and AgCl differ from those for CuCl, consistent with the lower solubility of AgCl.

Investigating the bio-rejuvenator effects on aged asphalt through exploring molecular evolution and chemical transformation of asphalt components during oxidative aging and regeneration

Using a rejuvenator to increase the dose of reclaimed asphalt pavement (RAP) materials in asphalt mixtures is a sustainable practice in the pavement industry. However, the mechanism by which the rejuvenator restores the performance of aged asphalt in the RAP binder remains an open question: research approaches are inadequate, and the details of asphalt aging are not clear. Here, we first revealed the aging mechanism of asphalt and obtained realistic structures of aged asphalt molecules by means of first-principles molecular simulations that modeled the chemical reaction between asphalt and oxygen. Subsequently, through classical modeling approaches that examine the solubility behaviors of asphalt molecules in n-heptane with and without a rejuvenator, we demonstrated the serious agglomeration of aged molecules, the transformation of aged resins into asphaltenes, and the restorative effect of the rejuvenator. To explore the driving force behind these findings, we performed density functional theory calculations and wavefunction analyses to determine the strength and nature of intermolecular interactions between asphalt molecules. The results indicated that the electrostatic interaction between aged asphalt molecules increases significantly upon generation of polar groups, and the rejuvenator decreases the electrostatic interaction mainly by eliminating hydrogen bonds, thus reducing molecular agglomeration, but has little effect on the dispersion force. Besides, Hansen solubility parameters were calculated to illustrate the agglomeration in aged asphalt and the restorative effect of the rejuvenator in terms of the “like-dissolves-like” rule. This study bridges the gap between electronic-scale modeling and complex engineering practice related to the aging and rejuvenation of asphalt.

Investigating the aging mechanism of asphaltene and its dependence on environmental factors through AIMD simulations and DFT calculations

To understand the complex aging mechanism of asphalt and its dependence on environmental factors, the chemical reactivity of asphaltene during aging under different environmental conditions was studied through first-principles molecular simulations and density functional theory calculations. The aging of asphaltene was demonstrated to involve a series of subreactions along different pathways on the asphaltene molecules, including hydrogen abstraction from carbon, formation of polar groups, aromatization of cycloalkanes, and homolysis of side chains. These subreactions occurred with different free-energy barriers and, therefore, had different kinetic rates. Asphaltene aging was found to be slightly accelerated in the presence of water owing to the improved electron transfer ability of the asphaltene molecule in an aqueous solvent. Under ultraviolet radiation, the asphaltene molecule transitioned to an excited state with an excitation energy of 348.7 kJ/mol, significantly increasing its aging rate. This work bridges the gap between electronic-scale modeling and diversified experimental observations related to asphalt aging and is expected to provide theoretical guidance for strategies to prevent or delay the aging-induced failure of asphalt pavements.

Post-processing of the planewave approximation of Schrödinger equations. Part I: linear operators

Abstract In this article we prove a priori error estimates for the perturbation-based post-processing of the plane-wave approximation of Schrödinger equations introduced and tested numerically in previous works (Cancès, Dusson, Maday, Stamm and Vohralík, (2014), A perturbation-method-based a posteriori estimator for the planewave discretization of nonlinear Schrödinger equations. C. R. Math., 352, 941--946; Cancès, Dusson, Maday, Stamm and Vohralík, (2016), A perturbation-method-based postprocessing for the planewave discretization of Kohn–Sham models. J. Comput. Phys., 307, 446--459.) We consider here a Schrödinger operator ${{\mathscr{H}} \,}= -\frac{1}{2}\varDelta +{\mathscr{V}}$ on $L^2(\varOmega )$, where $\varOmega $ is a cubic box with periodic boundary conditions and where ${\mathscr{V}}$ is a multiplicative operator by a regular-enough function ${\mathscr{V}}$. The quantities of interest are, on the one hand, the ground-state energy defined as the sum of the lowest $N$ eigenvalues of ${{\mathscr{H}} \,}$, and, on the other hand, the ground-state density matrix that is the spectral projector on the vector space spanned by the associated eigenvectors. Such a problem is central in first-principle molecular simulation, since it corresponds to the so-called linear subproblem in Kohn–Sham density functional theory. Interpreting the exact eigenpairs of ${{\mathscr{H}} \,}$ as perturbations of the numerical eigenpairs obtained by a variational approximation in a plane-wave (i.e., Fourier) basis we compute first-order corrections for the eigenfunctions, which are turned into corrections on the ground-state density matrix. This allows us to increase the accuracy by a factor proportional to the inverse of the kinetic energy cutoff ${E_{\textrm{c}}}^{-1}$ of both the ground-state energy and the ground-state density matrix in Hilbert–Schmidt norm at a low computational extra cost. Indeed, the computation of the corrections only requires the computation of the residual of the solution in a larger plane-wave basis and two fast Fourier transforms per eigenvalue.

Structure and chemistry of graphene oxide in liquid water from first principles

Graphene oxide is a rising star among 2D materials, yet its interaction with liquid water remains a fundamentally open question: experimental characterization at the atomic scale is difficult, and modeling by classical approaches cannot properly describe chemical reactivity. Here, we bridge the gap between simple computational models and complex experimental systems, by realistic first-principles molecular simulations of graphene oxide (GO) in liquid water. We construct chemically accurate GO models and study their behavior in water, showing that oxygen-bearing functional groups (hydroxyl and epoxides) are preferentially clustered on the graphene oxide layer. We demonstrated the specific properties of GO in water, an unusual combination of both hydrophilicity and fast water dynamics. Finally, we evidence that GO is chemically active in water, acquiring an average negative charge of the order of 10 mC m−2. The ab initio modeling highlights the uniqueness of GO structures for applications as innovative membranes for desalination and water purification.

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

CONSPECTUS: Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, have demonstrated a functional role of the ions for catalysis in numerous metallonucleases. Overall, the experimental data confirm the general mechanistic hypothesis for 2M-aided phosphoryl transfer originally reported by Steitz and Steitz ( Proc. Natl. Acad. Sci. U.S.A. 1993 , 90 ( 14 ), 6498 - 6502 ). This seminal paper proposed that one metal ion favors the formation of the nucleophile, while the nearby second metal ion facilitates leaving group departure during RNA hydrolysis. Both metals were suggested to stabilize the enzymatic transition state. Nevertheless, static X-ray structures alone cannot exhaustively unravel how the two ions execute their functional role along the enzymatic reaction during processing of DNA or RNA strands when moving from reactants to products, passing through metastable intermediates and high-energy transition states. In this Account, we discuss the role of multiscale molecular simulations in further disclosing mechanistic insights of 2M-aided catalysis for two prototypical enzymatic targets for drug discovery, namely, ribonuclease H (RNase H) and type II topoisomerase (topoII). In both examples, first-principles molecular simulations, integrated with structural data, emphasize a cooperative motion of the bimetal motif during catalysis. The coordinated motion of both ions is crucial for maintaining a flexible metal-centered structural architecture exquisitely tailored to accommodate the DNA or RNA sugar-phosphate backbone during phosphodiester bond cleavage. Furthermore, our analysis of RNase H and the N-terminal domain (PAN) of influenza polymerase shows that classical molecular dynamics simulations coupled with enhanced sampling techniques have contributed to describe the modulatory effect of metal ion concentration and metal uptake on the 2M mechanism and efficiency. These aspects all point to the emerging and intriguing role of additional adjacent ions potentially involved in the modulation of phosphoryl transfer reactions and enzymatic turnover in 2M-catalysis, as recently observed experimentally in polymerase η and homing endonuclease I-DmoI. These computational results, integrated with experimental findings, describe and reinforce the nascent concept of a functional and cooperative dynamics of the catalytic metal ions during the 2M-dependent enzymatic processing of DNA and RNA. Encouraged by the insights provided by computational approaches, we foresee further experiments that will feature the functional and joint dynamics of the catalytic metal ions for nucleic acid processing. This could impact the de novo design of artificial metallonucleases and the rational design of potent metal-chelating inhibitors of pharmaceutically relevant enzymes.

Thermodynamic properties calculation for MgO–SiO2 liquids using both empirical and first-principles molecular simulations

Both classical molecular dynamics simulations and first-principles molecular simulations were carried out to investigate the thermodynamic properties of MgO-SiO(2) melts at 4000 K and 0 GPa. After equilibrating both the mini-sized and large-sized systems using classical molecular dynamics simulations, several properties and structures were calculated and compared. Consistencies were found between results from mini-sized systems and those from large-sized systems. The first-principles molecular dynamics simulations were continued for 6 ps from several independent configurations output from the mini-sized systems. The enthalpy of mixing was calculated, and results were compared with those from empirical molecular simulations. We found that first-principles simulation modified the thermodynamic properties of silicate melts, and led to positive enthalpy of mixing at high SiO(2) concentrations and negative ones at low SiO(2) concentrations. Regressing data using the Margules equation led to results consistent with available references.

A combined DFT/Green’s function study on electrical conductivity through DNA duplex between Au electrodes

Electrical conducting properties of DNA duplexes sandwiched between Au electrodes have been investigated by use of first-principles molecular simulation based on DFT and Green’s function to elucidate the origin of their base sequence dependence. The theoretically simulated effects of DNA base sequence on the electrical conducting properties are in qualitative agreement with experiment. The HOMOs localized on Guanine bases have the major contribution to the electrical conductivity through DNA duplexes.

Effective radii of noble gas atoms in silicates from first-principles molecular simulation

An understanding of how noble gas atoms are dissolved in mantle minerals and melts is necessary to infer geological information from the constraints provided by noble gas geochemistry. For this purpose, first-principles molecular simulations are carried out on liquid and crystalline (stishovite) silica systems with dissolved noble gas atoms (He, Ne, Ar, Kr, and Xe). The first principles nature of the simulations, which do not involve empirical force field parameters, enables the determination of the effective radii and structural environments of the noble gas atoms. The noble gas atoms are shown to be highly compressible, so that their effective radii depend strongly on the molar volume of the system (which in turn depends on pressure). Due to the continuous nature of interatomic forces, the effective radii also depend on the extent to which the surrounding atoms can relax in response to the presence of the noble gas atom. In this regard, different definitions of effective radii are relevant in different situations: “equilibrium radii” that correspond to the optimal interatomic distances at the molar volume of the system, and “repulsive wall” radii that correspond to the interatomic distances where the interatomic potentials of mean force change from attractive to repulsive at that molar volume. The equilibrium radii determine the interatomic distances in a melt, and the repulsive wall radii determine the interatomic distances for interstitial sites in a crystal. Based on these effective radii, the structural environment surrounding the noble gas atoms at high pressure is shown to correspond to a close packing of O atoms around the central noble gas atom. Compression of the noble gas atoms is shown to correspond closely to the compression of the porosity within the silicate melt structure.