Ab Initio Quantum Mechanical Simulations Research Articles

Raman scattering of omphacite at high pressure: towards its possible application to elastic geothermobarometry

Abstract Due to their widespread occurrence in several geological settings, omphacite inclusions could be used for elastic Raman geothermobarometry. However, the Raman scattering of complex silicate minerals entrapped in a host depends on both the chemical composition and elastic strain developed during the metamorphic pathway, which makes the task very challenging. Here, as a very first step to probe the potential of omphacite to be used as a mineral inclusion in elastic geothermobarometry, we report the pressure dependence of the Raman spectra of omphacite crystals with the same composition, approximately Jd45Di55, but having different symmetry because of the existence (P2/n) or absence (C2/c) of chemical order at the six- and eight-coordinated cation sites. The experimental results are complemented by ab initio quantum mechanical simulations on fully ordered omphacite (Jd50Di50). We demonstrate that the position of the well-resolved Raman peak near 688 cm-1, arising from Si-O-Si bond bending, is very sensitive to pressure but independent of the state of chemical order, which makes it promising to be utilized in Raman geobarometry. The width of this peak varies with chemical order but not with pressure and therefore can be used to constrain the temperature of inclusion entrapment, because the chemical order is indicative of the closure temperature of the cation-exchange reaction. However, further detailed analyses on the compositional variation of the Raman spectra of omphacite is required before considering omphacite-in-garnet systems as suitable for Raman elastic geothermobarometry.

Deciphering Structural and Dynamical Properties of Hydrated Cobalt Porphyrins via Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation.

The present study successfully implemented the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism for the investigation of structural and dynamical properties of hydrated cobalt-porphyrin complexes. Considering the significance of cobalt ions in biological systems (for instance, vitamin B12), which reportedly incorporate cobalt ions in a d6, low spin, +3 state chelated in the corrin ring, an analog of porphyrin, the current study is focused on cobalt in the oxidation states +2 and +3 bound to the parent porphyrin lead structures embedded in an aqueous solution. These cobalt-porphyrin complexes were investigated in terms of their structural and dynamical properties at the quantum chemical level. The structural attributes of these hydrated complexes revealed the contrasting features of the water binding to these solutes, including a detailed evaluation of the associated dynamics. The study also yielded notable findings in regard to the respective electronic configurations vs coordination, which suggested that Co(II)-POR possesses a 5-fold square pyramidal coordination geometry in an aqueous solution containing the metal ion coordinating to four nitrogen atoms of the porphyrin ring and one axial water as the fifth ligand. On the other hand, high-spin Co(III)-POR was hypothesized to be more stable due to the smaller size-to-charge ratio of the cobalt ion, but the high-spin complex demonstrated unstable structural and dynamical behavior. However, the corresponding properties of the hydrated Co(III)LS-POR revealed a stable structure in an aqueous solution, thus suggesting the Co(III) ion to be in a low-spin state when bound to the porphyrin ring. Moreover, the structural and dynamical data were augmented by computing the free energy of water binding to the cobalt ions and the solvent-accessible surface area, which provide further information on thermochemical properties of the metal-water interaction and the hydrogen bonding potential of the porphyrin ring in these hydrated systems.

A Fourier-transformed feature engineering design for predicting ternary perovskite properties by coupling a two-dimensional convolutional neural network with a support vector machine (Conv2D-SVM)

In computational material sciences, Machine Learning (ML) techniques are now competitive alternatives that can be used in determining target properties conventionally resolved by ab initio quantum mechanical simulations or experimental synthesization. The successes realized with ML-based techniques often rely on the quality of the design architecture, in addition to the descriptors used in representing a chemical compound with good target mapping property. With the perovskite crystal structure at the forefront of modern energy materials discovery, accurately estimating related target properties is even of high importance due to the role such properties may have in defining the functionalization. As a result, the present study proposes a new feature engineering approach that takes advantage of both the direct ionic features and the periodic Fourier transformed reciprocal features of a three-dimensional perovskite polyhedral. The study is conducted on about 27,000 ABX3 perovskite structures with the stability energy, the formation energy, and the energy bandgap as targets. For accurate modeling, a feature-extracting two-dimensional convolutional neural network (Conv2D) is coupled with a prediction-enhancing Support Vector Machine (SVM) to form a hybridized Conv2D-SVM architecture. A comparison with previous benchmark evaluations reveals appreciable improvements in modeling accuracy for all target properties, particularly for the energy bandgap, for which the feature extraction approach yields 0.105 eV MAE, 0.301 eV RMSE, and 93.48% R2. Besides, the proposed design is further demonstrated to out-perform other similar periodic feature engineering approaches in the Coulomb matrix, Ewald-sum matrix, and Sine matrix, all in their absolute eigenvalue forms. All preprocessed data, source codes, and relevant sample calculations are openly available at: github.com/chenebuah/high_dim_descriptor.

A Multi-Scale Approach for Modeling the Optical Response of Molecular Materials Inside Cavities.

The recent fabrication advances in nanoscience and molecular materials point toward a new era where material properties are tailored in silico for target applications. To fully realize this potential, accurate and computationally efficient theoretical models are needed for: a) the computer-aided design and optimization of new materials before their fabrication; and b) the accurate interpretation of experiments. The development of such theoretical models is a challenging multi-disciplinary problem where physics, chemistry, and material science are intertwined across spatial scales ranging from the molecular to the device level, that is, from ångströms to millimeters. In photonic applications, molecular materials are often placed inside optical cavities. Together with the sought-after enhancement of light-molecule interactions, the cavities bring additional complexity to the modeling of such devices. Here, a multi-scale approach that, starting from ab initio quantum mechanical molecular simulations, can compute the electromagnetic response of macroscopic devices such as cavities containing molecular materials is presented. Molecular time-dependent density-functional theory calculations are combined with the efficient transition matrix based solution of Maxwell's equations. Some of the capabilities of the approach are demonstrated by simulating surface metal-organic frameworks -in-cavity and J-aggregates-in-cavity systems that have been recently investigated experimentally, and providing a refined understanding of the experimental results.

Fast inertial relaxation engine in the CRYSTAL code

In the framework of ab initio simulations, the search for energy minimum atomic structures is the first step to perform in studying the properties of a system. One of the most used and efficient optimization algorithms is a quasi-Newton line-search scheme based on the Broyden–Fletcher–Goldfarb–Shanno (Bfgs) Hessian updating formula. However, recent studies [Bitzek et al., Phys. Rev. Lett. 97, 170201 (2006) and Guénolé et al., Comput. Mater. Sci. 175, 109584 (2020)] suggested that minimization methods based on molecular dynamics concepts, such as the Fast Inertial Relaxation Engine (Fire) algorithm, often exhibit better performance and accuracy in finding local minima than line-search based schemes. In the present work, the implementation of Fire, in the framework of Crystal ab initio quantum mechanical simulation package [Dovesi et al., Wiley Interdiscip. Rev.: Comput. Mol. Sci. 8, e1360 (2018)], has been described. Its efficiency and performance in comparison with Bfgs quasi-Newton scheme have been assessed using Hartree–Fock and density functional theory with Perdew–Burke–Ernzerhof and hybrid functionals to model the potential energy surface. Fire shows good convergence behavior for all the considered systems, well reproducing the minimum energy structures obtained by the Bfgs approach. As regards the computational cost, Fire requires more iterations to converge with respect to Bfgs, but each Fire iteration is faster than the Bfgs one. The overall efficiency of Fire improves as the size of the system increased so that this minimization method seems to be very promising for systems without symmetry (space group P1) with a large number of atoms.

Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia

The impact of electron correlation in quantum mechanical charge field molecular dynamics (QMCF MD) simulations of Cu+ in pure liquid ammonia has been investigated by comparing the results obtained at the Hartree–Fock (HF) level and via resolution-of-identity second order Møller–Plesset perturbation theory (RIMP2). To achieve a manageable computational demand, a rigid-body solvent model was employed to describe the NH3 molecules. The solvation structures observed in both cases have similar characteristics in which tetrahedral [Cu(NH3)4]+ dominates with average CuN distances of 2.24 (HF) and 2.12 (RIMP2) Å, respectively. The ligand dynamics in the first solvation shell of the RIMP2 simulation are notably higher than in the HF case and resulted in the formation of an intermediate [Cu(NH3)3]+ complex along the sampling period. Electron correlation effects were found to mainly impact the solvent–solvent hydrogen bonding interaction, thereby providing a more accurate description of the structural properties in terms of the average CuN distances along with greatly enhanced ligand exchange dynamics occurring between the first and second solvation shell.

Intercalation voltages for spinel LixMn2O4 (0≤x≤2) cathode materials: Calibration of calculations with the ONETEP linear-scaling DFT code

Density functional theory (DFT) has become an engine for driving ab-initio quantum mechanical simulations spanning a vast range of applications. However, conventional DFT has limitations of the accessible system size due to computational expense. Recent progress on linear scaling DFT methods has enabled us to investigate larger systems. In this paper, we investigate the numerical agreement between conventional DFT codes and ONETEP, a linear-scaling DFT code, for important materials properties particularly calculating the intercalation potential of spinel electrode materials. Modulating materials with high energy density is an important aspect that contributes to the significant gap in our knowledge of the factors. We provide typical simulation results based on calculated intercalation potentials for discharging the spinel LixMn2O4, which plays a key role in developing high energy density lithium-ion batteries. The structural properties obtained after geometry optimisation with CASTEP yielded materials with volume within 3 % and lattice parameters within 1 % relative error with experimental values. The average intercalation potentials calculated with the CASTEP and ONETEP codes are within 3 % agreement with each other.

Absolute ion hydration free energy scale and the surface potential of water via quantum simulation

With a goal of determining an absolute free energy scale for ion hydration, quasi-chemical theory and ab initio quantum mechanical simulations are employed to obtain an accurate value for the bulk hydration free energy of the Na+ ion. The free energy is partitioned into three parts: 1) the inner-shell or chemical contribution that includes direct interactions of the ion with nearby waters, 2) the packing free energy that is the work to produce a cavity of size λ in water, and 3) the long-range contribution that involves all interactions outside the inner shell. The interfacial potential contribution to the free energy resides in the long-range term. By averaging cation and anion data for that contribution, cumulant terms of all odd orders in the electrostatic potential are removed. The computed total is then the bulk hydration free energy. Comparison with the experimentally derived real hydration free energy produces an effective surface potential of water in the range -0.4 to -0.5 V. The result is consistent with a variety of experiments concerning acid-base chemistry, ion distributions near hydrophobic interfaces, and electric fields near the surface of water droplets.

Efficient ab initio quantum mechanical simulations of structural stability and vibrational properties of bulk, monolayer and (n,0) nanotubes: Yttrium sesquioxide Y2O3

AbstractIn this contribution, we report reliable ab initio quantum mechanical simulations of a variety of physical properties concerning yttrium sesquioxide (Y2O3) in different arrangements from the bulk, the monolayer (h‐Y2O3), to the (n,0) single‐walled nanotubes in the range from n = 6 to 32, for geometry optimization and vibrational properties. Structural parameters, phonon wavenumbers, infrared (IR) and Raman intensities, and elastic constants are computed via density functional theory (DFT/B3LYP) where the trend towards the (h‐Y2O3) monolayer for large nanotube radius is discussed. We firstly report combined experimental and computational studies on the structural and vibrational properties of the bulk Y2O3. Then, IR and Raman spectra of all arrangements are simulated via the coupled perturbed Hartree–Fock and Kohn–Sham (CPHF/KS) computational schemes. For the (n,0) Y2O3 nanotube family, two sets of IR active phonon modes in the (200–400 cm−1) and (600–900 cm−1) ranges are determined. Both of them tend smoothly with different slope, towards the optical vibrational modes of the h‐Y2O3 single layer. Three sets of active phonon bands are obtained in their Raman spectrum. The first one, in the 0–100 cm−1 range contains two phonon modes, their vibration wavenumbers tend to zero at very large tube radius and are found to be connected to the elastic constants C11 and C66 of the h‐Y2O3 monolayer as the 1D → 2D transition is approached. The second one, in 200–400 cm−1 range tends to the optical mode E′ (ν = 308 cm−1) of the monolayer. The third set, in the 600–900 cm−1 range contains two active modes, their intensities tend to zero in the limit of large nanotube without change in their vibration wavenumbers.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03Å corresponding to a liquid ammonia density of 0.69g/mL at 235.16K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH3 interaction is weak electrostatically.

Highly Surface-Active Ca(OH)2 Monolayer as a CO2 Capture Material

Greenhouse gas emissions originating from fossil fuel combustion contribute significantly to global warming, and therefore the design of novel materials that efficiently capture CO2 can play a crucial role in solving this challenge. Here, we show that reducing the dimensionality of bulk crystalline portlandite results in a stable monolayer material, named portlandene, that is highly effective at capturing CO2. On the basis of theoretical analysis comprised of ab initio quantum mechanical calculations and force-field molecular dynamics simulations, we show that this single-layer phase is robust and maintains its stability even at high temperatures. The chemical activity of portlandene is seen to further increase upon defect engineering of its surface using vacancy sites. Defect-containing portlandene is capable of separating CO and CO2 from a syngas (CO/CO2/H2) stream, yet is inert to water vapor. This selective behavior and the associated mechanisms have been elucidated by examining the electronic structure, local charge distribution, and bonding orbitals of portlandene. Additionally, unlike conventional CO2 capturing technologies, the regeneration process of portlandene does not require high temperature heat treatment because it can release the captured CO2 by application of a mild external electric field, making portlandene an ideal CO2 capturing material for both pre- and postcombustion processes.

Revisiting structure and dynamics of Ag+ in 18.6% aqueous ammonia: An ab initio quantum mechanical charge field simulation

Structures and dynamics of Ag+ in 18.6% aqueous ammonia have been studied using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation at the Hartree–Fock (HF) level theory employing LANL2DZ ECP basis set for Ag+ and Dunning DZP for solvent molecules. Structural properties are in excellent agreement with previous QM/MM and experiments studies. [Ag(NH3)2(H2O)3]+ was found as dominant species during simulation time. For 20ps of simulation time, a labile first solvation shell was observed with both fast ammonia and water ligands exchanges. QMCF-MD framework describes first solvation shell more labile than conventional QM/MM MD simulation.

Classical molecular dynamics simulation of the interaction of hydrogen with defects in tungsten

The interaction of interstitial hydrogen (H) with dislocations and point defects in tungsten (W) is studied via numerical simulation within the framework of classical molecular dynamics (MD). Two alternative models are considered to describe the interatomic interactions: the embedded-atom method (EAM) and the bond-saturation model (the bond-order potential (BOP)). The calculated results are compared with data obtained via ab initio quantum-mechanical simulation. The potential developed recently within the framework of the EAM model demonstrated better agreement with the ab initio results than the BOP one. Molecular- statics calculations showed that hydrogen atoms are attracted by the dislocation core in both cases of screw and edge dislocations. The classical MD simulation of hydrogen diffusion in the vicinity of the edge dislocation demonstrated one-dimensional migration along the dislocation line.

An analysis of the influence of grain boundary strength on microstructure dependent fracture in polycrystalline tungsten

This work examines the influence of changes in grain boundary (GB) strength on microstructure dependent crack propagation in polycrystalline tungsten (W). The property of focus is brittleness index (BI) originally introduced by Evans and Marshall in 1976 and 1979, respectively, used in order to quantify the extent of brittleness of a material. In an earlier work, GBs of Ni-doped polycrystalline W have been characterized for embrittlement using ab-initio quantum mechanical simulations as a function of Ni atomic volume fraction and GB thickness. This work focuses on quantifying the influence of GB strength on microstructure dependent crack propagation. Continuum mechanical GB strength properties and effective W grain properties are derived from ab-initio simulation based stress–strain curves. The crack propagation simulations when GBs are considered of finite width are based on an extended finite element (XFEM) framework. Simulations that consider GBs of infinitesimal width due to mesh resolution issues are based on a combined XFEM-cohesive finite element model that employs cohesive elements at GBs. Analyses of crack propagation through finite width GBs focus on understanding the role of square root of length scale dimension in the original BI formulation. Based on analyses of crack propagation through finite width GBs oriented at angles varying from $$0^{\circ }\,\hbox {to}\,90^{\circ }$$ with respect to advancing crack, a quantitative criterion based on a failure index which predicts crack propagation path in polycrystalline W is proposed and examined.

Probing time-ordering in two-photon double ionization of helium on the attosecond time scale

We show that time ordering underlying time-dependent quantum dynamics is a physical observable accessible by attosecond streaking. We demonstrate the extraction of time ordering for the prototypical case of time-resolved two-photon double ionization of helium by an attosecond XUV pulse. The Eisenbud–Wigner–Smith time delay for the emission of a two-electron wavepacket and the time interval between subsequent emission events can be unambiguously determined by attosecond streaking. The delay between the two emission events sensitively depends on the energy, pulse duration, and angular distribution of the emitted electron pair. Our fully-dimensional ab initio quantum mechanical simulations provide benchmark data for experimentally accessible observables.

Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

Optical response of strongly absorbing inhomogeneous materials: Application to paper degradation

In this paper, we present a new noninvasive and nondestructive approach to recover scattering and absorption coefficients from reflectance measurements of highly absorbing and optically inhomogeneous media. Our approach is based on the Yang and Miklavcic theoretical model of light propagation through turbid media, which is a generalization of the Kubelka-Munk theory, extended to accommodate optically thick samples. We show its applications to paper, a material primarily composed of a web of fibers of cellulose, whose optical properties are strongly governed by light scattering effects. Samples studied were ancient and industrial paper sheets, aged in different conditions and highly absorbing in the ultraviolet region. The recovered experimental absorptions of cellulose fibers have been compared to theoretical ab initio quantum-mechanical computational simulations carried out within time-dependent density functional theory. In this way, for each sample, we evaluate the absolute concentration of different kinds of oxidized groups formed upon aging and acting as chromophores causing paper discoloration. We found that the relative concentration of different chromophores in cellulose fibers depends on the aging temperature endured by samples. This clearly indicates that the oxidation of cellulose follows temperature-dependent reaction pathways. Our approach has a wide range of applications for cellulose-based materials, like paper, textiles, and other manufactured products of great industrial and cultural interest, and can potentially be extended to other strongly absorbing inhomogeneous materials.

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

A single sodium chloride molecule in aqueous solution was simulated by the ab initio quantum mechanical charge field-molecular dynamics (QMCF-MD) approach. During a series of simulations the solvated molecule (CIP), dissociated solvated ions and - most noticeably - a solvent separated ion pair (SSIP) were observed and the structural and dynamical characteristics of these systems were investigated. In addition to a detailed structural analysis of the observed species, vibrational spectra and charge distributions were calculated to elucidate the mechanism of the NaCl dissociation.

Structure and dynamics of the Th4+-ion in aqueous solution – An ab initio QMCF-MD study

An ab initio quantum mechanical charge-field molecular dynamics simulation of the tetravalent thorium ion in aqueous environment is presented. Including the first and second hydration shell in the quantum mechanical treatment to enhance accuracy, this study yields very good results for a wide range of characteristics, as compared to experimental data. 20ps of simulation time were used to investigate structural and dynamical properties of the hydrate by numerous methods, including radial and angular distribution functions, three-body distribution functions, ligand exchange analysis and vibrational spectra. The hydrate proved stable during the simulation and did not show hydrolysis. The first solvation shell was found to be a very flexible one, with a number of intrashell ligand rearrangements occurring along the simulation. The data of the simulation also indicated the existence of a third hydration layer. Vibrational analysis yielded an average ion–oxygen frequency of 420cm−1, which is in excellent agreement with experimental data.

Rational synthesis of pindolol imprinted polymer by non-covalent protocol based on computational approach

Pindolol (PDL) is a potent and specific adrenoreceptor blocking agent. It is widely used in the treatment of hypertension, cardiac arrhythmia and angina pectoris. Molecularly imprinted polymers (MIPs) are synthetic receptors having potential applications in drug delivery systems and devices such as diagnostic sensors. In the present work, ab initio quantum mechanical simulations and computational screening were used to identify functional monomer having best interactions with PDL. A virtual library of 16 functional monomers was built and the possible minimum energy conformation of the monomers and PDL were calculated using Hartree-Fock (HF) method for the synthesis of PDL imprinted polymer. The interaction energy between functional monomer and the template were corrected by means of basis set superposition error (BSSE) in all pre-polymerization complexes. The hydrogen bonding between PDL and functional monomer was evaluated by changes in bond lengths before and after complex formation. The virtual template-monomer complex with highest interaction energy is more stable during the polymerization and leads to high selectivity and specificity toward the template. The interaction energy of PDL was found to be the highest with itaconic acid followed by 4-vinyl pyridine and least with acrylonitrile. Taking a spectroscopic viewpoint, results obtained from analysis of the harmonic infrared spectrum were examined. Red and blue shifts related to the stretching frequencies of either donors or acceptors of protons were identified and compared experimentally. Stoichiometric mole ratio of template to functional monomer was optimized and confirmed by UV visible spectra titrations. The theoretical results were correlated by evaluation of binding parameters of MIPs. The experimental binding results were in good agreement with theoretical computations.