Electronic Energy Calculations Research Articles

Breaking the size limitation of nonadiabatic molecular dynamics in condensed matter systems with local descriptor machine learning

Nonadiabatic molecular dynamics (NA-MD) is a powerful tool to model far-from-equilibrium processes, such as photochemical reactions and charge transport. NA-MD application to condensed phase has drawn tremendous attention recently for development of next-generation energy and optoelectronic materials. Studies of condensed matter allow one to employ efficient computational tools, such as density functional theory (DFT) and classical path approximation (CPA). Still, system size and simulation timescale are strongly limited by costly ab initio calculations of electronic energies, forces, and NA couplings. We resolve the limitations by developing a fully machine learning (ML) approach in which all the above properties are obtained using neural networks based on local descriptors. The ML models correlate the target properties for NA-MD, implemented with DFT and CPA, directly to the system structure. Trained on small systems, the neural networks are applied to large systems and long timescales, extending NA-MD capabilities by orders of magnitude. We demonstrate the approach with dependence of charge trapping and recombination on defect concentration in MoS2. Defects provide the main mechanism of charge losses, resulting in performance degradation. Charge trapping slows with decreasing defect concentration; however, recombination exhibits complex dependence, conditional on whether it occurs between free or trapped charges, and relative concentrations of carriers and defects. Delocalized shallow traps can become localized with increasing temperature, changing trapping and recombination behavior. Completely based on ML, the approach bridges the gap between theoretical models and realistic experimental conditions and enables NA-MD on thousand-atom systems and many nanoseconds.

Performance of range-separated long-range SOPPA short-range density functional theory method for vertical excitation energies.

In this paper, benchmark results are presented on the calculation of vertical electronic excitation energies using a long-range second-order polarization propagator approximation (SOPPA) description with a short-range density functional theory description based on the Perdew-Burke-Ernzerhof (PBE) functional. The excitation energies are investigated for 132 singlet states and 71 triplet states across 28 medium-sized organic molecules. The results show that overall SOPPA-srPBE always performs better than PBE and that SOPPA-srPBE performs better than SOPPA for singlet states, but slightly worse than SOPPA for triplet states when CC3 results are the reference values.

Building a New Platform for Significantly Improving Performance of Hartree-Fock and CCSD(T) Correlation Energy Based on Two-Point Complete Basis Set Extrapolation Schemes.

The leading cause of high expense in gold standard coupled cluster theory is that calculations of electronic energies converge exceedingly slowly with an increased basis set size. Extrapolation principally allows for achieving higher-quality outcomes at reduced costs. Numerous extrapolation formulas have been developed, with attempts to predict energies up to the complete basis set limit. Unfortunately, since the intricate shape of the function hinges on the molecular properties with the highest angular momentum of the basis set, the accuracy of the extrapolated energies highly depends on the fitted empirical parameters, which rely on the quality of the data sets for fitting. In this work, to overcome the extrapolation deficiency caused by the very limited data sets and smaller basis sets in the early stages, we constructed a new benchmark platform that includes a broader data set of 183 species (containing open-shell, closed-shell, ionic, and neutral species) and a larger basis set up to aug-cc-pV6Z. The newly optimized parameters can significantly improve the energy-predictive abilities of ten published formulas. Notably, all ten formulas perform quite similarly under the new platform with the reoptimized parameters. Finally, we built an online calculator for researchers to use for these extrapolation schemes. Our work would reignite the interest and applications of the underestimated formulas.

JEDI: A versatile code for strain analysis of molecular and periodic systems under deformation.

Stretching or compression can induce significant energetic, geometric, and spectroscopic changes in materials. To fully exploit these effects in the design of mechano- or piezo-chromic materials, self-healing polymers, and other mechanoresponsive devices, a detailed knowledge about the distribution of mechanical strain in the material is essential. Within the past decade, Judgement of Energy DIstribution (JEDI) analysis has emerged as a useful tool for this purpose. Based on the harmonic approximation, the strain energy in each bond length, bond angle, and dihedral angle of the deformed system is calculated using quantum chemical methods. This allows the identification of the force-bearing scaffold of the system, leading to an understanding of mechanochemical processes at the most fundamental level. Here, we present a publicly available code that generalizes the JEDI analysis, which has previously only been available for isolated molecules. Now, the code has been extended to two- and three-dimensional periodic systems, supramolecular clusters, and substructures of chemical systems under various types of deformation. Due to the implementation of JEDI into the Atomic Simulation Environment, the JEDI analysis can be interfaced with a plethora of program packages that allow the calculation of electronic energies for molecular systems and systems with periodic boundary conditions. The automated generation of a color-coded three-dimensional structure via the Visual Molecular Dynamics program allows insightful visual analyses of the force-bearing scaffold of the strained system.

Unveiling intermolecular mechanism and electronic properties between asphaltene and deep eutectic solvent for enhanced oil recovery using first principles calculation

Electronic structure and interaction energy calculations offer critical insights into non-bonded interactions in solute–solvent systems that can be used to extract heavy oil, particularly asphaltene, in enhanced oil recovery. The present study examines deep eutectic solvent (DES) interaction with asphaltene through first-principles calculations, revealing the role of hydrogen bonds, overall system stability, and its mechanism. The analysis reveals that the inclusion of asphaltene makes the DES-asphaltene structure less stable, i.e., increasing wettability with DES. DES formed non-bonded interactions with asphaltene's aliphatic segments but excluded aromatic rings due to strong π-π interactions. Among the studied DESs, DES1 (choline chloride and urea, 1:2 ratio) exhibited a strong interaction with asphaltene (-103.946 kJ/mol) and formed a hydrogen bond. All systems show negative binding energies, which indicate stability. Notably among them, DES2 (choline chloride and thiourea, 1:2) and DES3 (choline chloride and ethylene glycol, 1:2) displayed remarkable stability with asphaltene, evident in a widened band gap of 2.182 and 2.157 eV, respectively.

Non-thermal plasma mitigation of low concentration of air pollutants: removal of isopropyl alcohol using transition metal-oxide integration.

The present work studied the decomposition of isopropyl alcohol (IPA), widely used in chemical industries and households, in a packed-bed dielectric barrier discharge (DBD) plasma reactor. Metal oxide (MOx) coated on γ-Al2O3 (M = Cu, Mn, Co) was utilized for packing. The plasma-packed mode was a likely alternative to the conventional removal techniques, as it aids the conversion of dilute concentrations of IPA to CO and CO2 at ambient conditions (room temperature and atmospheric pressure). The mean electron energy calculations suggest that electrons with higher energy are generated when the discharge zone is packed with catalysts. When comparing IPA conversion (input concentration of 25ppm) for no packing mode and MOx/γ-Al2O3 coupled plasma mode, the latter method enhances conversion to greater than 90% at an applied voltage of 18kV. Also, MOx/γ-Al2O3 showed the highest selectivity to CO2 (70%) compared to plasma-only mode (45%). The metal-oxide layer provides the necessary catalytic surface facilitating the oxidation of IPA to COx through active oxygen species or the interaction of surface hydroxyl groups. The use of MOx/γ-Al2O3 resulted in about 90% carbon balance and reduced ozone generation, demonstrating the significance of integrating metal oxide to achieve efficient conversion and maximal selectivity towards the desired products.

High-Pressure Limit and Pressure-Dependent Rate Rules for β-Scission Reaction Class of Hydroperoxyl Alkyl Hydroperoxyl Radicals (•P(OOH)2) in Normal-Alkyl Cyclohexanes Combustion.

Chemical kinetic studies of the β-scission reaction class of hydroperoxyl alkyl hydroperoxyl radicals (•P(OOH)2) from normal-alkyl cyclohexanes are carried out systematically through high-level ab initio calculations. Geometry optimizations and frequency calculations for all species involved in the reactions are performed at the B3LYP/CBSB7 level of theory. Electronic single-point energy calculations are calculated at the CBS-QB3 level of theory. Rate constants for the reactions of β-scission, in the temperature range of 500-1500 K and the pressure range of 0.01-100 atm, are calculated using transition state theory (TST) and Rice-Ramsberger-Kassel-Marcus/Master-Equation (RRKM/ME) theory taking asymmetric Eckart tunneling corrections and the one-dimensional hindered rotor approximation into consideration. The rate rules are obtained by averaging the rate constants of the representative reactions of this class. These rate rules can greatly assist in constructing more accurate low-temperature combustion mechanisms for normal-alkyl cyclohexanes.

Theoretical and kinetic study of the H-atom abstraction reactions by Ḣ atom from alkyl cyclohexanes.

Reaction kinetics of hydrogen atom abstraction from six alkyl cyclohexanes, methyl cyclohexane (MCH), ethyl cyclohexane (ECH), n-propyl cyclohexane (nPCH), iso-propyl cyclohexane (iPCH), sec-butyl cyclohexane (sBCH) and iso-butyl cyclohexane (iBCH), by the Ḣ atom are systematically studied in this work. The M06-2X method combined with the 6-311++G(d,p) basis set is used to perform geometry optimization, frequency analysis and zero-point energy calculations for all species. The intrinsic reaction coordinate (IRC) calculations are performed to confirm the transition states connecting the reactants and products correctly. One-dimensional hindered rotors are used to treat the low frequency torsional models with potentials scanned at the M06-2X/6-31G level of theory. Electronic single-point energy calculations for all reactants, transition states, and products are performed at the QCISD(T)/CBS level of theory. High-pressure limiting rate constants of 39 reaction channels are obtained using conventional transition state theory with asymmetric Eckart tunneling corrections in the temperature range 298.15-2000 K. Reaction rate rules for H-atom abstraction by the Ḣ atom from alkyl cyclohexanes on primary, secondary and tertiary carbon sites on both the side chain and ring are provided. The obtained rate constants are given by the Arrhenius expression in the temperature range 500-2000 K, which can be used for the combustion kinetics model development for alkyl cyclohexanes.

PyBEST: Improved functionality and enhanced performance

PyBEST: Improved functionality and enhanced performance

Investigating the accuracy of density functional methods for molecules in electric fields.

The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical reactions has gained traction in recent years. Electronic structure calculations using OEEFs are commonly done using methods based on density functional theory (DFT), but until now, the performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more general scope. Looking at the accuracy of molecular geometries, electronic energies, and electric dipole moments compared to accurate coupled-cluster with perturbative triples data, we have investigated a wide variety of density functionals using different basis sets to determine how well the individual functionals perform on various types of chemical bonds. We found that most functionals accurately calculate geometries in OEEFs and that small basis sets are sufficient in many cases. Calculations of electronic energies show a significant error introduced by the OEEF, which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages that they bring.

Kinetic simulation of a 50 mTorr capacitively coupled argon discharge over a range of frequencies and comparison to experiments

The effect of driving frequency in the range of 13.56–73 MHz on electron energy distribution and electron heating modes in a 50 mTorr capacitively coupled argon plasma discharge is studied using 1D-3V particle-in-cell simulations. Calculated electron energy probability functions exhibit three distinct “temperatures” for low-, mid-, and high-energy electrons at all the studied driving frequencies. When compared to published experimental data, the calculated probability functions show a reasonable agreement for the energy range resolved in the measurements (about 2–10 eV). Discrepancies due to limitations in experimental energy resolution outside this range lead to differences between computational and experimental values of the electron number density determined from the distribution functions, and the predicted effective electron temperature is within 25% of experimental values. The impedance of the discharge is interpreted in terms of a homogeneous equivalent circuit model, and the driving frequency dependence of the inferred combined sheath thickness is found to obey a known, theoretically derived, power law. The average power transferred from the field to the electrons (electron heating) is computed, and a region of negative heating near the sheath edge, particularly at higher driving frequencies, is identified. Analysis of the electron momentum equation shows that electron inertia, which on temporal averaging would be zero in a linear regime, is responsible for negative values of power deposition near the sheath edge at high driving frequencies due to the highly nonlinear behavior of the discharge.

Synthesis, crystal structure, computational studies, and antioxidant properties of dimethylformamide-bound magnesium tetraphenylporphyrin

The synthesis, characterization and crystal structure of a dimethylformamide (DMF) coordinated magnesium tetraphenylporphyrin, [Mg(TPP)(DMF)]·CH2Cl2 (1), is described. Theoretical studies including optimization of the geometry, simulation of the electronic spectrum and binding energy calculations were performed for the complexes using the DFT method to understand the axial coordination in magnesium porphyrins. To get insight into intermolecular interactions Hirshfeld surface analyses and plotting of the 2D fingerprint was performed. Antioxidant activity was measured for the complex which showed enhanced antioxidant activity in the presence of DMF.

Fractional Charge Density Functional Theory and Its Application to the Electro-inductive Effect

We employed the chemical potential equalization principle to demonstrate that fractional electrons are involved in the electro-inductive effect as well as the vibrational Stark effect. By the chemical potential model, we were able to deduce that the frontier molecular orbitals of immobilized molecules can provide valuable insight into these effects. To further understand and quantify these findings, we introduced fractional charge density functional theory (FC-DFT), a canonical ensemble approach for open systems. This method allows for the calculation of electronic energies, nuclear gradients, and the Hessian matrix of fractional electronic systems. To correct the spurious delocalization error commonly found in approximate density functionals for small systems, we imposed the Perdew-Parr-Levy-Balduz (PPLB) condition through linear interpolation of two adjacent integer points (LI-FC-DFT). Although this approach is relatively simple in terms of molecular modeling, the results obtained through LI-FC-DFT calculations predict the same trend seen in experimental reactivity and the frequency change of immobilized molecules.

First-principles calculations to investigate structural, elastic, electronic, optical, and magnetic properties of Hg2WO4 for photocatalytic applications

In the present work, structural, elastic, electronic, optical, and magnetic properties of Hg2WO4 are investigated using CASTEP simulation tool. Generalized Gradient Approximation (GGA) along with Perdew-Burke-Ernzerhof (PBE) are employed for the calculation of electronic exchange and correlation energy. In structural analysis, Hg2WO4 is found to be stable with C-centered monoclinic structure having space group C2/c. Material’s ductile nature is confirmed with Pugh’s approximation where calculated B/G ratio is greater than 0.75 and Frantsevich’s rule where v is greater than 0.26. The calculations of electronic properties show that Hg2WO4 has indirect band gap of 2.14 eV. While the optical study reveals that Hg2WO4 has a good photosensitivity in visible light region. Furthermore, the spin-polarized treatment shows that Hg2WO4 is antiferromagnetic in nature. The current findings can be of great importance for the development of efficient photocatalytic materials for water splitting and associated applications.

Understanding the migration mechanism of hydrogen atom from the α-Fe matrix into nano-precipitates via DFT calculations.

The service of high-strength steel suffers from the threat of hydrogen embrittlement and introducing nano-precipitates is an effective avenue to mitigate it. How hydrogen atoms migrate into nano-precipitates is an important question that needs to be clarified. In this study, NEB-based DFT calculations have clearly constructed the energy evolution profiles of the whole process for hydrogen atoms diffusing from α-Fe through the α-Fe/MC (M = V, Ti, Nb) coherent interfaces and finally into the nano-precipitates. The calculation results indicate that a hydrogen atom migrates with difficulty through the α-Fe/MC coherent interfaces and the diffusions in nano-precipitates follow two-step pathways. The C atom vacancy is easier to form in MC nano-precipitates. When introducing a C atom or metallic atom vacancy into the α-Fe/MC interface, the C atom vacancy is the hydrogen trapping site, while the metallic atom vacancy reduces the migration barrier. In addition, once a C atom or metallic atom vacancy is formed in the nano-precipitate, the vacancy will behave as an irreversible trapping site. Finally, electronic structure analyses and distortion energy calculations clearly reveal the effects of the local atomic environment on hydrogen diffusion from α-Fe into nano-precipitates.

Initial unimolecular decomposition of 3,4-bis(3-fluorodinitromethylfuroxan-4-yl) furoxan from quantum mechanics and ReaxFF molecular dynamics simulation

High-energy-density materials (HEDMs) have a wide range of applications in many usages. Recently synthesized 3,4-bis(3-fluorodinitromethylfuroxan-4-yl) furoxan (BFTF-1), composed of furoxan rings and fluorodinitromethyl groups, has shown advanced properties comparing to other existed HEDMs, such as density and enthalpy of formation. Understanding the decomposition mechanism for BFTF-1 could provide insights into future designs of HEDMs, and the initial decompositions are critical steps in the mechanism. In the present study, we employed quantum mechanics calculations and reactive molecular dynamics simulations to explore the initial decomposition steps. The electronic structural analysis and bond dissociation energy calculations suggested that the nitro moieties in the fluorodinitromethyl groups and the furoxan rings could begin the bond breaking process in BFTF-1. The reactive molecular dynamics simulation showed that the increase of the nitro moieties was concurrent with the decrease of BFTF-1, proving the nitro moieties were the first product for the decomposition of BFTF-1. The present study laid the ground for the theoretical understanding of decomposition mechanisms for BFTF-1 and shed light on further designs of advanced HEDMs.

A comprehensive study on the electronic structure, dielectric and optical properties of alkali-earth metals and transition metal hydroxides M(OH)2.

In the present work, the physical properties of alkali-earth metal and transition metal hydroxides are comprehensively investigated using the density functional theory. Here, the alkali-earth metals Ca, Mg, and transition metals Cd, Zn are considered from the II-A and II-B groups in the periodic table of elements. The first principle electronic structure calculations show that these bulk hydroxide materials are direct band gap material. Ca(OH)2 and Mg(OH)2 exhibit an insulating behavior with a very large band gap. However, Cd(OH)2 and Zn(OH)2 are found to be wide band gap semiconductors. The dielectric and optical studies reveal that these materials have a high degree of anisotropy. Hence, the light propagation in these materials behaves differently in the direction perpendicular and parallel to the optical axis, and exhibits birefringence. Therefore, these materials may be useful for optical communication. The calculated electron energy loss suggests that these materials can also be used for unwanted signal noise suppression. The wide band gap makes them useful for high-power applications. Moreover, Ca(OH)2 and Mg(OH)2 are found to be suitable for dielectric medium.

A CGA-ONIOM-DFT framework for accurate and efficient determination of thermodynamics and Kinetics: Case study of cyclopentane reaction with hydroxyl radical

Accurate and efficient determination of thermodynamics and kinetics is long pursued but hindered by electronic energy calculations due to very high computational cost. In this work, we propose a Cascaded Group Additivity (CGA)-ONIOM-DFT framework targeting fast thermodynamic and kinetic predictions. We studied the reaction of cyclopentane with OH radical as a proof-of-principle demonstration. The CGA-ONIOM method accurately constructed the potential energy surface with a mean unsigned error of 0.20 kcal∙mol-1 compared to the full-level CCSD(T)/CBS results. The calculated rate constants agree well with the experimental data, suggesting the feasibility of using the CGA-ONIOM-DFT framework for combustion chemical kinetics.

Magnetic Field Effect on the Oxidation of Unsaturated Compounds by Molecular Oxygen

A quantum-chemical analysis of the effect of a constant magnetic field on radical formation in the processes of chain oxidation of organic compounds by molecular oxygen is presented. The calculation of the total electronic energies and thermodynamic functions of the compounds involved in the reactions was performed by the density functional method with the hybrid exchange-correlation functional of Becke, Lee, Yang and Parr DFT B3LYP/6-311G** using the NWChem software package. The effect of the magnetic field on the individual stages of chain oxidation is associated with the evolution of radical pairs. It is assumed that the dipole–dipole interaction in a radical pair is not averaged by the diffusion of radicals and should be taken into account. To a large extent, the magnetic field effect (MFE) value is influenced by the ratio between the relaxation time of the oscillatory-excited state in the radical pair (tvib) and the relaxation time of the inter-combination transitions (tst). Although the developed technique refers to liquid-phase reactions, it can be used to study the MFE for oxidation of biologically significant compounds in multiphase systems, such as micelles, liposomes and membranes.

Facile MOF-derived one-pot synthetic approach toward Ru single atoms, nanoclusters, and nanoparticles dispersed on CeO2 supports for enhanced ammonia synthesis

The Haber-Bosch process for NH3 production is one of the largest global energy consumers. Despite improvements over the past century, developing catalysts with enhanced activities and durabilities remains challenging. Ru-based catalysts supported on CeO2 are suitable alternatives under mild reaction conditions. Here, we elucidated the effects of Ru structure on the physicochemical properties and catalytic activities of Ru-CeO2 systems. One-pot syntheses with metal–organic frameworks as sacrificial templates were used to prepare Ru single-atom, nanocluster, and nanoparticle systems. The Ru nanoclusters and single atoms exhibited superior and more stable performances toward NH3 production, with no hydrogen poisoning, in relation to the Ru nanoparticles. Kinetic data and electronic energy calculations demonstrated that the Ru nanoclusters coexisting with Ru single atoms may maximize the NH3 synthetic activity via the combination of dissociative and associative mechanisms. These results provide guidance for the rational design and optimization of Ru-based catalysts for use in NH3 synthesis.