Electronic Structure Data Research Articles

Enhancing Eyringpy: Accurate Rate Constants with Canonical Variational Transition State Theory and the Hindered Rotor Model.

The recrossing effect and hindered rotations can lead to significant inaccuracies in rate constant calculations using transition state theory and the harmonic oscillator approximation. To address these issues, we enhanced Eyringpy, a Python-based computational tool, by integrating the canonical variational transition state theory (CVT) and the hindered rotor model, effectively mitigating the limitations of traditional methods. CVT rate constants are calculated using electronic structure data from nonstationary points along the minimum-energy path. Additionally, we developed an algorithm based on reaction force analysis to autonomously select relevant nonstationary points. Torsions are modeled using one-dimensional hindered rotor approaches proposed by Pitzer-Gwinn and Ayala-Schlegel.

Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials.

A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot's entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C-C-C angle, thereby allowing rupture at lower bond strains. We extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick-slip phenomena upon tightening and similar points of failure.

Kinetics and Mechanism of the Singlet Oxygen Atom Reaction with Dimethyl Ether.

We combine in situ laser spectroscopy, quantum chemistry, and kinetic calculations to study the reaction of a singlet oxygen atom with dimethyl ether. Infrared laser absorption spectroscopy and Faraday rotation spectroscopy are used for the detection and quantification of the reaction products OH, H2O, HO2, and CH2O on submillisecond time scales. Fitting temporal profiles of products with simulations using an in-house reaction mechanism allows product branching to be quantified at 30, 60, and 150 Torr. The experimentally determined product branching agrees well with master equation calculations based on electronic structure data and transition state theory. The calculations demonstrate that the dimethyl peroxide (CH3OOCH3) generated via O-insertion into the C-O bond undergoes subsequent dissociation to CH3O + CH3O through energetically favored reactions without an intrinsic barrier. This O-insertion mechanism can be important for understanding the fate of biofuels leaking into the atmosphere and for plasma-based biofuel processing technologies.

Fragment Orbitals Extracted from First-Principles Plane-Wave Calculations.

Decomposing extended structures into smaller, molecular, even functional groups or simple fragments has a long tradition in chemistry because it allows for understanding certain electronic peculiarities in truly chemical terms. By doing so, invaluable property information is chemically accessible, for example, needed to rationalize catalytic or magnetic or optical nature. In order to also follow that train of thought for periodic materials, we have developed a tool which in a straightforward manner derives fragment molecular orbitals from plane-wave electronic-structure data of whatever kind of solid-state material. We here report on the mathematical apparatus of the method dubbed linear combination of fragment orbitals (LCFO) used for that purpose, implemented within the LOBSTER code. The method is illustrated from various sorts of molecular entities contained in such crystalline materials, together with an assessment of both accuracy and robustness of the new tool.

Pretraining of attention-based deep learning potential model for molecular simulation

Machine learning-assisted modeling of the inter-atomic potential energy surface (PES) is revolutionizing the field of molecular simulation. With the accumulation of high-quality electronic structure data, a model that can be pretrained on all available data and finetuned on downstream tasks with a small additional effort would bring the field to a new stage. Here we propose DPA-1, a Deep Potential model with a gated attention mechanism, which is highly effective for representing the conformation and chemical spaces of atomic systems and learning the PES. We tested DPA-1 on a number of systems and observed superior performance compared with existing benchmarks. When pretrained on large-scale datasets containing 56 elements, DPA-1 can be successfully applied to various downstream tasks with a great improvement of sample efficiency. Surprisingly, for different elements, the learned type embedding parameters form a spiral in the latent space and have a natural correspondence with their positions on the periodic table, showing interesting interpretability of the pretrained DPA-1 model.

Ultrafast Excited-State Nonadiabatic Dynamics in Pt(II) Donor-Bridge-Acceptor Assemblies: A Quantum Approach for Optical Control.

The ultrafast nonadiabatic excited state dynamics of (PTZ-N-benzyl-acetylide) (trans-bis-trimethylphosphine) Pt(II) (acetylide-NDI-bis-methyl) 1, representative of a series of Pt(II) donor-bridge-acceptor assemblies experimentally studied by the Weinstein group, University of Sheffield, is investigated by means of wavepacket propagations based on the multiconfiguration time-dependent Hartree (MCTDH) method. On the basis of electronic structure data obtained at the time-dependent density functional theory (TD-DFT) level, the subpicosecond decay is simulated by solving an 11 electronic states multimode problem, up to 18 vibrational normal modes, including both spin-orbit coupling (SOC) and vibronic coupling. A careful analysis of the results, within the diabatic representation, provides the key features of the spin-vibronic mechanism at work in this complex, distinguishing between the spin-orbit and vibronically activated ultrafast processes within the excited states manifold. The knowledge of the key active normal modes that promote selectively the population of specific electronic excited states opens a route toward optical control by selectively exciting these modes in order to drive the associated nonadiabatic processes. Relevant simulations, over 2 ps, are proposed to assess the impact of these selective vibrational excitations on the branching ratio between the primary photoproducts, namely, bridge-acceptor charge-transfer (CT) and donor-acceptor charge-separated (CS) electronic states. Whereas the excitation of the localized acetylide bridge C≡C bond stretching does not modify drastically the population of the low-lying electronic states within the first two ps, vibrational excitation of the out-of-plane twisting motion of the N-benzyl group linked to the donor entity favors the population of the 1,3CS states at the expense of the lowest 1,3CT states. This quantum study opens the route to IR optical control experiments based on the specific alteration of vibrational normal modes that activate vibronic couplings between key electronic excited states. However, the presence of critical crossings along the PES channels associated with these normal modes and the role of concurrent SOC driven ultrafast transfers of population should not be underestimated.

Hybrid Steroid‐[60]Fullerene as n‐Type Material for Organic Photovoltaics

AbstractFullerene derivatives have been used as electron acceptor and transport materials in organic photovoltaics as well as in perovskite solar cells. Among them, [6,6]‐phenyl‐C61‐butyric acid methyl ester (PC61BM) has been one of the most widely used, in combination with poly‐3‐hexylthiophene (P3HT) as an electron donor semiconducting polymer, for the fabrication of organic bulk heterojunction solar cells (BHJ‐OSC). In this work, a steroid‐fullerene hybrid was synthesized through the Bingel–Hirsch reaction to compare its properties with PC61BM as the reference structure. Different spectroscopic techniques were employed to characterize the new fullerene derivative, namely 1D and 2D nuclear magnetic resonance (NMR), Fourier Transform Infrared Spectroscopy (FTIR), and high‐resolution mass spectrometry (HRMS). In addition, thermogravimetric analysis (TGA), and cyclic voltammetry were also performed. The characterization was completed by transmission electron microscopy (TEM), which explore the hybrid‘s morphology, where the presence of the steroid moiety increases the solubility of the fullerene material. DFT/PBE−D3(BJ)/6‐311G(d,p) calculations for both the steroid‐fullerene hybrid and PC61BM allowed to obtain geometry optimizations and electronic structure data. A comparative study to analyze the nature of the electronic properties of the synthesized steroid‐[60]fullerene hybrid and PC61BM with an oligomer of ten thiophene units, used in the active layer of organic solar cells, was carried out. Electron density maps using the [CIS|CNDOL/21] approach illustrate the photoexcitation of the donor followed by an electron‐charge transfer to the acceptor fullerene.

Toward a Unified Analytical Description of Internal Conversion and Intersystem Crossing in the Photodissociation of Thioformaldehyde. I. Diabatic Singlet States.

The photodissociation of thioformaldehyde is an archetypal system for the study of competition between internal conversion and intersystem crossing, which involves its two singlet states (S0 and S1) and two triplet states (T1 and T2). In order to perform accurate dynamic simulations, either quantum or quasi-classical, it is essential to construct an analytical representation for all necessary electronic structure data. In this work, a diabatic potential energy matrix (DPEM), Hd, for the two singlet states (S0 and S1) is reported. The analytical form of DPEM is symmetrized and constructed to reproduce adiabatic energies, energy gradients, and derivative couplings obtained from high-level multireference configuration interaction wave functions. The Hd is fully saturated in the molecular configuration space with a trajectory-guided point sampling approach. This Hd can provide the accurate description of the photodissociation of thioformaldehyde on its singlet states and is also a necessary part for incorporating the spin-orbit couplings into a unified diabatic framework. Preliminary quasi-classical trajectory simulations show that a roaming mechanism also exists in the molecular dissociation channel of thioformaldehyde.

Assessing Mixed Quantum-Classical Molecular Dynamics Methods for Nonadiabatic Dynamics of Molecules on Metal Surfaces.

Mixed quantum-classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional models for the scattering of diatomic molecules at metal surfaces based on recently published electronic structure data. We apply several MQC methods to investigate their ability to capture how nonadiabatic effects influence molecule-metal energy transfer during the scattering process. Specifically, we compare molecular dynamics with electronic friction, Ehrenfest dynamics, independent electron surface hopping, and the broadened classical master equation approach. In the case of independent electron surface hopping, we implement a simple decoherence correction approach and assess its impact on vibrationally inelastic scattering. Our results show that simple, low-dimensional models can be used to qualitatively capture experimentally observed vibrational energy transfer and provide insight into the relative performance of different MQC schemes. We observe that all approaches predict similar kinetic energy dependence but return different vibrational energy distributions. Finally, by varying the molecule-metal coupling, we can assess the coupling regime in which some MQC methods become unsuitable.

Rutile, anatase, brookite and titania thin film from Hubbard corrected and hybrid DFT

As a benchmark, the structural, electronic and optical properties of the three main phases of TiO2 crystals have been calculated using Hubbard U correction and hybrid functional methods in density-functional theory. These calculations are compared concerning the available experimental observations on pristine TiO2 crystals. Modified hybrid functionals, particularly the PBE0 functional with 11.4% fraction of exact exchange, are shown to provide highly accurate atomic structures and also accurate electronic structure data, including optical excitation energies. With DFT + U, accurate optical spectra are also possible, but only if the Hubbard U is applied on the O 2p electrons exclusively. Furthermore, both methods, the 11.4%-PBE0 hybrid functional and the DFT + U p scheme have been used to study TiO2 amorphous ultra-thin films, confirming the agreement of the two methods even with respect to small details of the optical spectra. Our results show that the proposed DFT + U p methodology is computationally efficient, but still accurate. It can be applied to well-ordered TiO2 polymorphs as well as to amorphous TiO2 and will allow for the calculations of complex titania-based structures.

Self-Consistent Chemical Pressure Analysis: Resolving Atomic Packing Effects through the Iterative Partitioning of Space and Energy.

While planewave DFT methods offer capabilities to calculate the relative stabilities and many physical properties exhibited by solid state structures, their detailed numerical output does not easily map onto the often empirical concepts and parameters used by synthetic chemists or materials scientists. The DFT-chemical pressure (CP) method is an approach to bridging this divide by explaining or anticipating a variety of structural phenomena in terms of atomic size and packing effects, but its reliance on adjustable parameters has limited the method's predictive potential. In this article, we present the self-consistent (sc)-DFT-CP analysis, in which the criterion of self-consistency is used to automatically solve these parameterization issues. We begin by illustrating the need for this improved method with the results for a series of CaCu5-type/MgCu2-type intergrowth structures, where unphysical trends emerge that have no clear structural origin. To address these challenges, we derive iterative treatments for assigning ionicity and for the partitioning of the EEwald + Eα terms in the DFT total energy into homogeneous and localized terms. In this method, self-consistency is achieved between the input and output charges from a variation of the Hirshfeld charge scheme, while the partitioning of the EEwald + Eα terms is adjusted to create equilibrium between the net atomic pressures calculated within atomic regions and from the interatomic interactions. The behavior of the sc-DFT-CP method is then tested using electronic structure data for several hundred compounds from the Intermetallic Reactivity Database. Finally, we return to the CaCu5-type/MgCu2-type intergrowth series with the sc-DFT-CP approach, showing that trends in the series are now easily traced to changes in the thicknesses of the CaCu5-type domains and lattice mismatch at the interface. Through this analysis and the complete update to the CP schemes in the IRD, the sc-DFT-CP method is demonstrated as a theoretical tool for the investigation of atomic packing issues across intermetallic chemistry.

Local spectroscopy of a gate-switchable moiré quantum anomalous Hall insulator

In recent years, correlated insulating states, unconventional superconductivity, and topologically non-trivial phases have all been observed in several moiré heterostructures. However, understanding of the physical mechanisms behind these phenomena is hampered by the lack of local electronic structure data. Here, we use scanning tunnelling microscopy and spectroscopy to demonstrate how the interplay between correlation, topology, and local atomic structure determines the behaviour of electron-doped twisted monolayer–bilayer graphene. Through gate- and magnetic field-dependent measurements, we observe local spectroscopic signatures indicating a quantum anomalous Hall insulating state with a total Chern number of ±2 at a doping level of three electrons per moiré unit cell. We show that the sign of the Chern number and associated magnetism can be electrostatically switched only over a limited range of twist angle and sample hetero-strain values. This results from a competition between the orbital magnetization of filled bulk bands and chiral edge states, which is sensitive to strain-induced distortions in the moiré superlattice.

Predicting the properties of NiO with density functional theory: Impact of exchange and correlation approximations and validation of the r2SCAN functional

Transition metal oxide materials are of great utility, with a diversity of topical applications ranging from catalysis to electronic devices. Because of their widespread importance in materials science, there is increasing interest in developing computational tools capable of reliable prediction of transition metal oxide phase behavior and properties. The workhorse of materials theory is density functional theory (DFT). Accordingly, we have investigated the impact of various correlation and exchange approximations on their ability to predict the properties of NiO using DFT. We have chosen NiO as a particularly challenging representative of transition metal oxides in general. In so doing, we have provided validation for the use of the r2SCAN density functional for predicting the materials properties of oxides. r2SCAN yields accurate structural properties of NiO and a local spin moment that notably persists under pressure, consistent with experiment. The outcome of our study is a pragmatic scheme for providing electronic structure data to enable the parameterization of interatomic potentials using state-of-the-art artificial intelligence (AI) and machine learning (ML) methodologies. The latter is essential to allow large scale molecular dynamics simulations of bulk and surface materials phase behavior and properties with ab initio accuracy.

Incorporating Polarization and Charge Transfer into a Point-Charge Model for Water Using Machine Learning

Rigid nonpolarizable water models with fixed point charges have been widely employed in molecular dynamics simulations due to their efficiency and reasonable accuracy for the potential energy surface. However, the dipole moment surface of water is not necessarily well-described by the same fixed charges, leading to failure in reproducing dipole-related properties. Here, we developed a machine-learning model trained against electronic structure data to assign point charges for water, and the resulting dipole moment surface significantly improved the predictions of the dielectric constant and the low-frequency IR spectrum of liquid water. Our analysis reveals that within our atom-centered point-charge description of the dipole moment surface, the intermolecular charge transfer is the major source of the peak intensity at 200 cm-1, whereas the intramolecular polarization controls the enhancement of the dielectric constant. The effects of exact Hartree-Fock exchange in the hybrid density functional on these properties are also discussed.

First-principles calculations: Structural stability, electronic structure, optical properties and thermodynamic properties of AlBN2, Al3BN4 and AlB3N4 nitrides

In this work, using first-principles calculations based on density functional theory were performed to predict the structural stability, electronic structure, optical properties and thermodynamic properties of three nitrides (AlBN2, Al3BN4 and AlB3N4). The calculated formation enthalpies of AlBN2, Al3BN4, and AlB3N4 are −5.369, −6.108, and −5.630 eV/atom, respectively, suggesting that the structures of these three nitrides are stable. By calculating the phonon spectrum and phonon density of states, it can be known that the three nitrides are dynamically stable. The electronic structure data reveal that the band gaps of AlBN2, Al3BN4, and AlB3N4 are 3.35, 3.05, and 3.59 eV, respectively. The polycrystalline and directional optical properties are discussed, and the AOPT of AlBN2 is [0.99, 0.99], indicating its optical anisotropy. Finally, a detailed examination of thermodynamic parameters reveals that Al3BN4 has the most stable thermodynamic properties, and the order of stability is: Al3BN4 > AlB3N4 > AlBN2.

Phosphine Reactivity and Its Implications for Pyrolysis Experiments and Astrochemistry

Despite the importance of phosphorus-bearing molecules for life and their abundance outside Earth, the chemistry of those compounds still is poorly described. The present study investigates phosphine (PH3) decomposition and formation pathways. The reactions studied include phosphine thermal dissociation, conversion into PO(2Π), PN(1Σ+), and reactions in the presence of H2O+. The thermodynamic and rate coefficients of all reactions are calculated in the range of 50-2000 K considering the CCSD(T)/6-311G(3df,3pd)//ωB97xD/6-311G(3df,3pd) electronic structure data. The rate coefficients were calculated by RRKM and semiclassical transition-state theory (SCTST). According to our results, PH3 is stable to thermal decomposition at T < 100 K and can be formed promptly by a reaction network involving PH(3Σ-), PO(2Π), and PN(1Σ+). In the presence of radiation or ions, PH3 is readily decomposed. For this reason, it should be mainly associated with dust grains or icy mantles to be observed under the physical conditions prevailing in the interstellar medium (ISM). The intersystem crossing associated with the dissociation of the isomers PON, NPO, and PNO is accessed by multireference methods, and its importance for the gas-phase PH3 formation/destruction is discussed. Also, the implications of the present outcomes on phosphorus astrochemistry are highlighted.

Computed spectroscopic properties of HCN, HNC, and all their D, 13C, and 15N substituted isotopologues

ABSTRACT Starting from ab initio electronic structure data, we develop parametrized analytic potential energy surfaces for the HCN and HNC isomers by variationally calculating rovibrational energy levels and adjusting the potential parameters so as to get agreement with experimentally derived transition frequencies to within about 1 cm−1. We also determine an analytic expression in terms of molecular parameters to effortlessly calculate the rovibrational energy levels. We use the obtained empirical potentials to calculate rovibrational levels for eight isotopologues of HCN and eight of HNC up to about 4000 cm−1 above the ground state. The energy levels are estimated to be accurate to within about 3 cm−1 based on comparison to experimental rovibrational transition frequencies for H12C14N, H12C14N, H13C14N, and H12C15N. For all 16 isotopologues, we calculate the zero-point energy and in nine cases we can compare with experimentally derived values. In these comparisons, the variationally obtained ZPE is within 5 cm−1 of the experimentally derived value, while the closed expression gives values within 6 cm−1 of the experimental values. For all 16 isotopologues, we also give molecular parameters from which the energy levels can easily be calculated using the closed expression. Endo- and exoergicities are given for 12 isotopic exchange reactions involving HCN/HNC and some isotopologues together with pre-exponential factors that should be useful in future modelling studies of rare isotopologues.

Data-Driven Many-Body Potential Energy Functions for Generic Molecules: Linear Alkanes as a Proof-of-Concept Application.

We present a generalization of the many-body energy (MB-nrg) theoretical/computational framework that enables the development of data-driven potential energy functions (PEFs) for generic covalently bonded molecules, with arbitrary quantum mechanical accuracy. The "nearsightedness of electronic matter" is exploited to define monomers as "natural building blocks" on the basis of their distinct chemical identity. The energy of generic molecules is then expressed as a sum of individual many-body energies of incrementally larger subsystems. The MB-nrg PEFs represent the low-order n-body energies, with n = 1-4, using permutationally invariant polynomials derived from electronic structure data carried out at an arbitrary quantum mechanical level of theory, while all higher-order n-body terms (n > 4) are represented by a classical many-body polarization term. As a proof-of-concept application of the general MB-nrg framework, we present MB-nrg PEFs for linear alkanes. The MB-nrg PEFs are shown to accurately reproduce reference energies, harmonic frequencies, and potential energy scans of alkanes, independently of their length. Since, by construction, the MB-nrg framework introduced here can be applied to generic covalently bonded molecules, we envision future computer simulations of complex molecular systems using data-driven MB-nrg PEFs, with arbitrary quantum mechanical accuracy.

Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values.

Classical molecular dynamics simulations are a versatile tool in the study of biomolecular systems, but they usually rely on a fixed bonding topology, precluding the explicit simulation of chemical reactivity. Certain modifications can permit the modeling of reactions. One such method, multiscale reactive molecular dynamics, makes use of a linear combination approach to describe condensed-phase free energy surfaces of reactive processes of biological interest. Before these simulations can be performed, models of the reactive moieties must first be parametrized using electronic structure data. A recent study demonstrated that gas-phase electronic structure data can be used to derive parameters for glutamate and lysine which reproduce experimental pKa values in both bulk water and the staphylococcal nuclease protein with remarkable accuracy and transferability between the water and protein environments. In this work, we first present a new model for aspartate derived in similar fashion and demonstrate that it too produces accurate pKa values in both bulk and protein contexts. We also describe a modification to the prior methodology, involving refitting some of the classical force field parameters to density functional theory calculations, which improves the transferability of the existing glutamate model. Finally and most importantly, this reactive molecular dynamics approach, based on rigorous statistical mechanics, allows one to specifically analyze the fundamental physical causes for the marked pKa shift of both aspartate and glutamate between bulk water and protein and also to demonstrate that local steric and electrostatic effects largely explain the observed differences.

Tuning structure and magnetic properties of table-like magnetocaloric effect in Er6MnSb2 by zirconium substitution

In this study, zirconium (Zr) successfully substituted for erbium (Er) in Er6–xZrxMnSb2 (x = 0, 0.5, 1, 1.5) of the Fe2P type, with comprehensive characterizations on crystal structure, electronic structure and magnetic properties. According to synchrotron powder X-ray diffraction data analysis and density functional theory calculation, Zr does not randomly but preferentially occupy during the doping process and results in weaker magnetic exchange interactions and depressed ordering temperatures. The electronic structure data show that the doping of Zr can weaken interaction between Er and Mn atoms. Owing to multiple transitions, the Er6–xZrxMnSb2 (x = 0, 0.5, 1, 1.5) exhibit table-like magnetocaloric effect. Er6MnSb2 displays wide δTFWHM (full width at half maximum of the magnetic entropy change curve) of 116 K and high relative cooling power of 388.62 J/kg for 3 T. The maximum magnetic entropy change of Er6–xZrxMnSb2 is increased from 3.81 to 7.69 J/(kg·K) with the Zr content up from x = 0 to x = 1.5.