Quantum Mechanical Density Research Articles

Nitrogen-Containing Gas Sensing Properties of 2-D Ti2N and Its Derivative Nanosheets: Electronic Structures Insight.

In this work, the potentials of two-dimensional Ti2N and its derivative nanosheets Ti2NT2(T=O, F, OH) for some harmful nitrogen-containing gas (NCG) adsorption and sensing applications have been unveiled based on the quantum-mechanical Density Functional Theory calculations. It is found that the interactions between pure Ti2N and NCGs (including NO, NO2, and NH3 in this study) are very strong, in which NO and NO2 can even be dissociated, and this would poison the substrate of Ti2N monolayer and affect the stability of the sensing material. For the monolayer of Ti2NT2(T=O, F, OH) that is terminated by functional groups on surface, the adsorption energies of NCGs are greatly reduced, and a large amount of charges are transferred to the functional group, which is beneficial to the reversibility of the sensing material. The significant changes in work function imply the good sensitivity of the above mentioned materials. In addition, the fast response time further consolidates the prospect of two-dimensional Ti2NT2 as efficient NCGs’ sensing materials. This theoretical study would supply physical insight into the NCGs’ sensing mechanism of Ti2N based nanosheets and help experimentalists to design better 2-D materials for gas adsorption or sensing applications.

Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density

Reaction barriers are key to our understanding of chemical reactivity and catalysis. Certain reactions are so seminal in chemistry that countless variants, with or without catalysts, have been studied, and their barriers have been computed or measured experimentally. This wealth of data represents a perfect opportunity to leverage machine learning models, which could quickly predict barriers without explicit calculations or measurement. Here, we show that the topological descriptors of the quantum mechanical charge density in the reactant state constitute a set that is both rigorous and continuous and can be used effectively for the prediction of reaction barrier energies to a high degree of accuracy. We demonstrate this on the Diels-Alder reaction, highly important in biology and medicinal chemistry, and as such, studied extensively. This reaction exhibits a range of barriers as large as 270 kJ/mol. While we trained our single-objective supervised (labeled) regression algorithms on simpler Diels-Alder reactions in solution, they predict reaction barriers also in significantly more complicated contexts, such a Diels-Alder reaction catalyzed by an artificial enzyme and its evolved variants, in agreement with experimental changes in kcat. We expect this tool to apply broadly to a variety of reactions in solution or in the presence of a catalyst, for screening and circumventing heavily involved computations or experiments.

Vibrational spectroscopy, quantum computational and molecular docking studies on 2-chloroquinoline-3-carboxaldehyde

The quantum mechanical density functional theory (DFT) approach was used to analyze vibrational spectroscopy for the title compound 2-chloroquinoline-3-carboxaldehyde, and the observations were compared to experimental results. B3LYP with the 6–311++ G (d, p) basis set produces the optimized molecular structure and vibrational assignments. The charge delocalization and hyper conjugative interactions were studied using NBO analysis. Fukui functions were used to determine the chemical reactivity of the examined molecule. The linear polarizability, first order polarizability, NLO and Thermodynamic properties are calculated. Additionally, Molecular electrostatic potential (MEP) and HOMO-LUMO are reported. Multi wavefunction analysis like ELF (Electron Localization Function) and LOL (Localized Orbital Locator) are analyzed. For the headline compound, drug-likeness properties were examined. Molecular docking analysis on the examined molecule are done to understand the biological functions of the headline molecule and the minimum binding energy, hydrogen bond interactions, are analyzed.

Unravelling the performance of oxycarbonyl-thiocarbamate collectors on chalcopyrite using first-principles calculations and micro-flotation recoveries

First-principle quantum mechanical density functional theory (DFT) was employed to explore the bonding behaviour, adsorption energies and electronic properties directly related to the reactivity’s of O-butyl-N-ethoxycarbonyl-thiocarbamate (BECTC), O-isobutyl-N-ethoxycarbonyl-thiocarbamate (IBECTC), O-butyl-N-butoxycarbonyl-thiocarbamate (BBCTC), O-isobutyl-N-butoxycarbonyl-thiocarbamate (IBBCTC), and O-isobutyl-N-isobutoxycarbonyl-thiocarbamate (IBIBCTC) with the chalcopyrite (CuFeS2) (112) surface and complimented by micro-flotation recoveries of the chalcopyrite. The partial density of states (PDOS) of the isolated oxycarbonyl-thiocarbamate collector showed that the sulphur atom (S1) was more active and will be more reactive during adsorption. Adsorption of the oxycarbonyl-thiocarbamate collectors preferred the Cu atom over Fe atoms. The adsorption energies and micro-flotation recoveries yielded similar trends and the order followed: BBCTC > IBIBCTC > BECTC > IBBCTC > IBECTC, which showed that BBCTC exhibited the strongest exothermic adsorption. This showed that the adsorption energies that determined how a collector binds to the mineral surface can predict the flotation recoveries. The PDOS and atomic population charges after adsorption showed that both Cu and S1 atoms lose charges (electron donor) forming σ-bonds, and simultaneously, dative π-bonds. The results also showed that BBCTC and BECTC are better collectors for the selective flotation of chalcopyrite minerals and indicated that a straight hydrocarbon chain gave stronger adsorption than a branched hydrocarbon chain.

Phonon-Assisted Ballistic Current from First-Principles Calculations.

The bulk photovoltaic effect (BPVE) refers to current generation due to illumination by light in a homogeneous bulk material lacking inversion symmetry. In addition to the intensively studied shift current, the ballistic current, which originates from asymmetric carrier generation due to scattering processes, also constitutes an important contribution to the overall kinetic model of the BPVE. In this Letter, we use a perturbative approach to derive a formula for the ballistic current resulting from the intrinsic electron-phonon scattering in a form amenable to first-principles calculation. We then implement the theory and calculate the ballistic current of the prototypical BPVE material BaTiO_{3} using quantum-mechanical density functional theory. The magnitude of the ballistic current is comparable to that of the shift current, and the total spectrum (shift plus ballistic) agrees well with the experimentally measured photocurrents. Furthermore, we show that the ballistic current is sensitive to structural change, which could benefit future photovoltaic materials design.

The advanced treatment of hydrogen bonding in quantum crystallography.

Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

Diamantanethiols on Metal Surfaces: Spatial Configurations, Bond Dissociations, and Polymerization.

We report the on-surface chemistry of diamantanethiols on metal surfaces by combining low-temperature STM studies with quantum mechanical density functional theory computations. First, we examined the spatial configurations of diamantanethiols on metal surfaces, in which the thiol-substrate confinement plays a key role. We then thermally desorbed the diamantanethiols from the substrate surfaces to determine whether the C-S or S-metal bonds preferentially break. Finally, we explored diamantane-4,9-dithiol and its polymerization on metal surfaces, forming linear nanodiamond disulfur chains. This work broadens the fundamental knowledge of functionalized diamondoid behavior on surfaces and provides a novel approach to link diamantane as necklace-chain nanodiamond hybrid materials.

Photoluminescence line shapes for color centers in silicon carbide from density functional theory calculations

Silicon carbide with optically and magnetically active point defects offers unique opportunities for quantum technology applications. Since interaction with these defects commonly happens through optical excitation and de-excitation, a complete understanding of their light-matter interaction in general and optical signatures, in particular, is crucial. Here, we employ quantum mechanical density functional theory calculations to investigate the photoluminescence lineshapes of selected, experimentally observed color centers (including single vacancies, double vacancies, and vacancy impurity pairs) in 4H-SiC. The analysis of zero-phonon lines as well as Huang-Rhys and Debye-Waller factors are accompanied by a detailed study of the underlying lattice vibrations. We show that the defect lineshapes are governed by strong coupling to bulk phonons at lower energies and localized vibrational modes at higher energies. Generally, good agreement to the available experimental data is obtained, and thus we expect our theoretical work to be beneficial for the identification of defect signatures in the photoluminescence spectra and thereby advance the research in quantum photonics and quantum information processing.

A Review of Many-Body Interactions in Linear and Nonlinear Plasmonic Nanohybrids

In this review article, we discuss the many-body interactions in plasmonic nanohybrids made of an ensemble of quantum emitters and metallic nanoparticles. A theory of the linear and nonlinear optical emission intensity was developed by using the many-body quantum mechanical density matrix method. The ensemble of quantum emitters and metallic nanoparticles interact with each other via the dipole-dipole interaction. Surfaces plasmon polaritons are located near to the surface of the metallic nanoparticles. We showed that the nonlinear Kerr intensity enhances due to the weak dipole-dipole coupling limits. On the other hand, in the strong dipole-dipole coupling limit, the single peak in the Kerr intensity splits into two peaks. The splitting of the Kerr spectrum is due to the creation of dressed states in the plasmonic nanohybrids within the strong dipole-dipole interaction. Further, we found that the Kerr nonlinearity is also enhanced due to the interaction between the surface plasmon polaritons and excitons of the quantum emitters. Next, we predicted the spontaneous decay rates are enhanced due to the dipole-dipole coupling. The enhancement of the Kerr intensity due to the surface plasmon polaritons can be used to fabricate nanosensors. The splitting of one peak (ON) two peaks (OFF) can be used to fabricate the nanoswitches for nanotechnology and nanomedical applications.

Explorations on the electronic structure and spectroscopic IR assignments of 5-methyl-2-(2-oxopropyl)-pyrazolo[5,1-b]quinazolin-9(3H)-one molecule

In the present work, theoretical investigations on a quinazoline derivate, 5-methyl-2-(2-oxopropyl)pyrazolo[5,1-b]quinazolin-9(3H)-one, have been carried out through quantum mechanical density functional B3LYP/6-31G(d,p) method to explore its electronic structure and vibrational features. The normal modes analysis was executed to predict the contributions of different vibrational modes at the required frequencies in the infrared region and the spectral peaks have been assigned accordingly. Besides, certain electronic properties that are associated with chemical reactivity like, HOMO-LUMO energy gap, molecular electrostatic potential, Mulliken partial charges, etc have been estimated and discussed herein. It has been established that the molecule is chemically reactive and may be used in designing drugs as COX-2/5-LOX inhibitor.

Time-dependent momentum expectation values from different quantum probability and flux densities.

Based on the Ehrenfest theorem, the time-dependent expectation value of a momentum operator can be evaluated equivalently in two ways. The integrals appearing in the expressions are taken over two different functions. In one case, the integrand is the quantum mechanical flux density j̲, and in the other, a different quantity j̲̃ appears, which also has the units of a flux density. The quantum flux density j̲ is related to the probability density ρ via the continuity equation, and j̲̃ may as well be used to define a density ρ̃ that fulfills a continuity equation. Employing a model for the coupled dynamics of an electron and a proton, we document the properties of the densities and flux densities. It is shown that although the mean momentum derived from the two quantities is identical, the various functions exhibit a very different coordinate and time-dependence. In particular, it is found that the flux density j̲̃ directly monitors temporal changes in the probability density, and the density ρ̃ carries information about wave packet dispersion occurring in different spatial directions.

Spatially Inhomogeneous Distribution of the Quantum Mechanical Current Density at the Sub-Barrier Reflection of the Electron Wave from the Potential Step in the 2D Nanostructure

In this paper, the influence of the interference of electron waves during their reflection from a rectangular semi-infinite potential barrier to the spatial distribution of quantum mechanical current density еjx(x, z) (e is the electron charge and jx(x, z) is the flow of probability density) in a semiconductor 2D nanostructure is theoretically studied. The structure consists of narrow and wide rectangular quantum wells (QWs) arranged successively along the direction of electron wave propagation. It is assumed that the wave falls from narrow QW1 on a potential barrier of height V0 in wide QW2. It is shown that when a wave with energy less than V0 falls on the barrier, then, in certain conditions, spatially inhomogeneous distribution $$ej_{x}^{{\left( 1 \right)}}(x,z)$$ oscillating in a complicated way exists in QW1. An exponential attenuation and coordinate dependent leakage $$ej_{x}^{{\left( 2 \right)}}(x,z)$$ under the barrier may occur in QW2. It is shown that this behavior of $$ej_{x}^{{\left( 1 \right)}}(x,z)$$ and $$ej_{x}^{{\left( 2 \right)}}(x,z)$$ is caused by the interference of electron waves propagating through different quantum-dimensional subbands in the considered nanostructure.

Heterogeneous Intramolecular Electric Field as a Descriptor of Diels-Alder Reactivity.

External electric fields have proven to be an effective tool in catalysis, on par with pressure and temperature, affecting the thermodynamics and kinetics of a reaction. However, fields in molecules are complicated heterogeneous vector objects, and there is no universal recipe for grasping the exact features of these fields that implicate reactivity. Herein, we demonstrate that topological features of the heterogeneous electric field within the reactant state and of the quantum mechanical electron density-a scalar reporter on the field experienced by the system-can be identified as rigorous descriptors of the reactivity to follow. We scrutinize specifically the Diels-Alder reaction. Its 3D nature and the lack of a singular directionality of charge movement upon barrier crossing make the effect of the electric field not obvious. We show that the electric field topology around the dienophile double bond and the associated changes in the topology of the electron density in this bond are predictors of the reaction barrier. They are also the metrics to rationalize and predict how the external field would inhibit or enhance the reaction. The findings pave the way toward designing external fields for catalysis and reading the reactivity without an explicit mechanistic interrogation, for a variety of reactions.

Electron-Passing Neural Networks for Atomic Charge Prediction in Systems with Arbitrary Molecular Charge.

Atomic charges are critical quantities in molecular mechanics and molecular dynamics, but obtaining these quantities requires heuristic choices based on atom typing or relatively expensive quantum mechanical computations to generate a density to be partitioned. Most machine learning efforts in this domain ignore total molecular charges, relying on overfitting and arbitrary rescaling in order to match the total system charge. Here, we introduce the electron-passing neural network (EPNN), a fast, accurate neural network atomic charge partitioning model that conserves total molecular charge by construction. EPNNs predict atomic charges very similar to those obtained by partitioning quantum mechanical densities but at such a small fraction of the cost that they can be easily computed for large biomolecules. Charges from this method may be used directly for molecular mechanics, as features for cheminformatics, or as input to any neural network potential.

Coarse-Grained Simulation of the Adsorption of Water on Au(111) Surfaces Using a Modified Stillinger-Weber Potential.

For reproducing the behavior of water molecules adsorbed on gold surfaces in terms of density of both bulk and interfacial water and in terms of structuring of water on top of gold atoms, the implementation of a multibody potential is necessary, thus the Stillinger–Weber potential was tested. The goal is using a single nonbonded potential for coarse-grained models, without the usage of explicit charges. In order to modify the angular part of the Stillinger–Weber potential from a single cosine to a piecewise function accounting for multiple equilibrium angles, employed for Au–Au–Au and Au–Au–water triplets, it is necessary to create a version of the simulation package LAMMPS that supports the assignment of multiple favored angles. This novel approach is able to reproduce the data obtained using quantum mechanical calculations and density profiles of both bulk and adsorbed water molecules obtained using classical polarizable force fields.

Inelastic Neutron Scattering Investigation of MgCl2 Nanoparticle-Based Ziegler–Natta Catalysts for Olefin Polymerization

The effect of nanosize and structural disorder on the MgCl2 support of Ziegler–Natta catalysts has been investigated in terms of induced changes to their vibrational spectroscopic fingerprint. In particular, the inelastic neutron scattering (INS) technique was used, which allowed sampling of the whole lattice dynamics of the support. The experimental INS spectra of several ball-milled, polycrystalline, samples of MgCl2 were collected for the first time and were compared to simulated spectra from quantum-mechanical density functional theory calculations. Theoretical calculations were performed on a variety of MgCl2 structural models: (i) ordered and disordered bulk (3D); (ii) low-dimensional structures such as surfaces (2D) and nanorods (1D); and nanoclusters (0D). This allowed us to link specific features of the spectra to specific changes in the atomic structure and dynamics of the catalyst support. In particular, the effect of translational symmetry breaking and rotational disorder is discussed. Furthermore, the present data suggest that the ball-milling process mostly leads to the formation of bulk-like crystallites rather than nanoparticles. This work ultimately highlights the combined use of INS measurements and quantum-mechanical simulations as an effective approach for the atomistic characterization of defective (nano)materials.

Michler’s hydrol blue elucidates structural differences in prion strains

Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler's hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs.

Structure and properties of amorphous uranium dioxide

Amorphous uranium dioxide (UO2) has been modelled on the atomic scale using a combination of quantum mechanical (density functional theory) and classical forcefield methods (molecular dynamics and reverse Monte-Carlo). The atomic scale structure of the amorphous state has been predicted and is presented in the form of simulated X-ray diffraction patterns, pair correlation functions and bond angle distributions. These are shown to be consistent with the experimental patterns previously reported. To enable accurate calculation of the energies and magnetic properties, using quantum mechanics, reverse Monte-Carlo was used to generate reduced cells from larger molecular dynamic melt-quenches. This allowed density functional theory energy minimisation for structures consistent with the amorphous state. Building on this, the material's propensity to deviate from stoichiometry, the magnetic structure and amorphous UO2 surface energy were computed. Non-stoichiometry is accommodated more readily in the amorphous system than in crystalline UO2. This indicates that deviations from stoichiometry in fuel (for example as a result of operation) will be accommodated at amorphous phases, if present, leaving a more stoichiometric crystalline phase – impacting processes including fission gas mobility, melting points and a number of other safety relevant properties. The magnetic structure of bulk amorphous UO2 is predicted to be a spin-glass, unlike crystalline UO2 which has anti-ferromagnetic ordering at 0 K. The surface energy of amorphous UO2 is computed to be 0.79 Jm−2, which is similar to the experimentally observed surface energy of grain boundary bubbles in UO2 and comparable to the surface energies reported for crystalline UO2. Results are pertinent to ongoing efforts to understand the nature of grain boundaries in nuclear fuels, to model fission gas release from them, radiation induced amorphization and the impact of dopants and impurities on nuclear fuel's manufacture and in-reactor behaviour.

Profiling SARS-CoV-2 Main Protease (MPRO) Binding to Repurposed Drugs Using Molecular Dynamics Simulations in Classical and Neural Network-Trained Force Fields.

The current COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2 urgently calls for a working therapeutic. Here, we report a computation-based workflow for efficiently selecting a subset of FDA-approved drugs that can potentially bind to the SARS-CoV-2 main protease MPRO. The workflow started with docking (using Autodock Vina) each of 1615 FDA-approved drugs to the MPRO active site. This step selected 62 candidates with docking energies lower than −8.5 kcal/mol. Then, the 62 docked protein–drug complexes were subjected to 100 ns of molecular dynamics (MD) simulations in a molecular mechanics (MM) force field (CHARMM36). This step reduced the candidate pool to 26, based on the root-mean-square-deviations (RMSDs) of the drug molecules in the trajectories. Finally, we modeled the 26 drug molecules by a pseudoquantum mechanical (ANI) force field and ran 5 ns hybrid ANI/MM MD simulations of the 26 protein–drug complexes. ANI was trained by neural network models on quantum mechanical density functional theory (wB97X/6-31G(d)) data points. An RMSD cutoff winnowed down the pool to 12, and free energy analysis (MM/PBSA) produced the final selection of 9 drugs: dihydroergotamine, midostaurin, ziprasidone, etoposide, apixaban, fluorescein, tadalafil, rolapitant, and palbociclib. Of these, three are found to be active in literature reports of experimental studies. To provide physical insight into their mechanism of action, the interactions of the drug molecules with the protein are presented as 2D-interaction maps. These findings and mappings of drug–protein interactions may be potentially used to guide rational drug discovery against COVID-19.

A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method

Here, the development of a method for analyzing the electrostatic complementarity of protein-protein interactions (PPIs) using fully quantum mechanical electron density (EDN) and electrostatic potential (ESP) is described. Partial EDN (pEDN) and ESP (pESP) of each protein were newly defined based on the fragment molecular orbital method. Illustrative calculations were performed for programmed cell death-1 (PD-1) and its ligand (PD-L1), which showed that the electrostatic complementarity of PD-1 and PD-L1 was clearly represented by the pEDN and pESP. Further analysis revealed that electrostatic complementarity induced by complex formation is important for binding between the proteins.