Ab Initio Calculations Research Articles

Triplet State Radical Chemistry: Significance of the Reaction of 3SO2 with HCOOH and HNO3.

The triplet excited states of sulfur dioxide can be accessed in the UV region and have a lifetime large enough that they can react with atmospheric trace gases. In this work, we report high level ab initio calculations for the reaction of the a3B1 and b3A2 excited states of SO2 with weak and strong acidic species such as HCOOH and HNO3, aimed to extend the chemistry reported in previous studies with nonacidic H atoms (water and alkanes). The reactions investigated in this work are very versatile and follow different kinds of mechanisms, namely, proton-coupled electron transfer (pcet) and conventional hydrogen atom transfer (hat) mechanisms. The study provides new insights into a general and very important class of excited-state-promoted reactions, opening up interesting chemical perspectives for technological applications of photoinduced H-transfer reactions. It also reveals that atmospheric triplet chemistry is more significant than previously thought.

Machine-Learning driven STM images prediction of doped/defective graphene: Towards optimized tools for 2D nanomaterials characterization

Scanning tunneling microscopy (STM) is a key characterization technique that allows for visualization of specific features at nanostructures, given its ability to reveal changes in local charge densities in doping or defective sites. Besides the experimental acquisition of STM data from real samples, there is the theoretical route, which allows for STM images simulation from ab-initio calculations on defined nanostructures. This work presents an alternative route for theoretical STM image prediction by means of Machine Learning (ML) methods, based on the training of deep convolutional neural networks using simulated STM data. The ML-based STM predictions for defective, B- and N-doped graphene quantum dots are compared to ab-initio STM simulations, in terms of accuracy of structural rearrangements, charge density localizations, and computational resources requirements. The results demonstrate that STM images predicted by ML-methods are accurate at doping sites, whereas they show good similarity to simulations of large structural vacancies. This work represents a novel alternative for the use of ML methods in image-based characterization routines of doped/defective graphene, and potentially, for other 2-dimensional nanomaterials.

EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment.

Atomic partial charges are crucial parameters in molecular dynamics simulation, dictating the electrostatic contributions to intermolecular energies and thereby the potential energy landscape. Traditionally, the assignment of partial charges has relied on surrogates of ab initio semiempirical quantum chemical methods such as AM1-BCC and is expensive for large systems or large numbers of molecules. We propose a hybrid physical/graph neural network-based approximation to the widely popular AM1-BCC charge model that is orders of magnitude faster while maintaining accuracy comparable to differences in AM1-BCC implementations. Our hybrid approach couples a graph neural network to a streamlined charge equilibration approach in order to predict molecule-specific atomic electronegativity and hardness parameters, followed by analytical determination of optimal charge-equilibrated parameters that preserve total molecular charge. This hybrid approach scales linearly with the number of atoms, enabling for the first time the use of fully consistent charge models for small molecules and biopolymers for the construction of next-generation self-consistent biomolecular force fields. Implemented in the free and open source package EspalomaCharge, this approach provides drop-in replacements for both AmberTools antechamber and the Open Force Field Toolkit charging workflows, in addition to stand-alone charge generation interfaces. Source code is available at https://github.com/choderalab/espaloma-charge.

Understanding the cavity Born-Oppenheimer approximation.

Experiments have demonstrated that vibrational strong coupling between molecular vibrations and light modes can significantly change molecular properties, such as ground-state reactivity. Theoretical studies toward the origin of this exciting observation can roughly be divided into two categories, with studies based on Hamiltonians that simply couple a molecule to a cavity mode via its ground-state dipole moment on the one hand, and on the other hand ab initio calculations that self-consistently include the effect of the cavity mode on the electronic ground state within the cavity Born-Oppenheimer (CBO) approximation; these approaches are not equivalent. The CBO approach is more rigorous, but unfortunately it requires the rewriting of electronic-structure code, and its results may sometimes be hard to physically interpret. In this work, we exploit the relation between the two approaches and demonstrate on a real molecule (hydrogen fluoride) that for realistic coupling strengths, we can recover CBO energies and spectra to high accuracy using only out-of-cavity quantities from standard electronic-structure calculations. In doing so, we discover what thephysical effects underlying the CBO results are. Our methodology can aid in incorporating more possibly important features in models, play a pivotal role in demystifying CBO results, and provide a practical and efficient alternative to full CBO calculations.

ABLRI: A program for calculating the long-range interaction energy between two monomers in their non-degenerate states.

An accurate description of the long-range (LR) interaction is essential for understanding the collision between cold or ultracold molecules. However, to our best knowledge, there lacks a general approach to construct the intermolecular potential energy surface (IPES) between two arbitrary molecules and/or atoms in the LR region. In this work, we derived analytical expressions of the LR interaction energy, using the multipole expansion of the electrostatic interaction Hamiltonian and the non-degenerate perturbation theory. To make these formulae practical, we also derived the independent Cartesian components of the electrostatic properties, including the multipole moments and polarizabilities, of the monomer for a given symmetry using the properties of these components and the group-theoretical methods. Based on these newly derived formulae, we developed a FORTRAN program, namely ABLRI, which is capable of calculating the interaction energy between two arbitrary monomers both in their non-degenerate electronic ground states at large separations. To test the reliability of this newly developed program, we constructed IPESs for the electronic ground state of H2O-H2 and O2-H systems in the LR region. The interaction energy computed by our program agreed well with the abinitio calculation, which shows the validity of this program.

Ab-initio transport model to study the thermoelectric performance of MoS2, MoSe2, and WS2 monolayers by using Boltzmann transport equation

The potential for thermoelectric applications of two-dimensional materials is quite promising. Using ab-initio calculations, we have investigated the electronic band structure, phonon band structure, electronic density of states, and phonon density of states of monolayers MoS2, MoSe2, and WS2. In order to compute the thermoelectric properties of monolayers MoS2, MoSe2, and WS2, we used the ab-initio model suggested by Faghaninia et al (2015 Phys. Rev. B 91 235123). Within this model, by using inputs from density functional theory and considering all relevant elastic and inelastic scattering mechanisms, we have calculated the thermoelectric properties of monolayers MoS2, MoSe2, and WS2 over various ranges of temperature (T) and carrier concentration (n). The obtained results of Seebeck coefficients (S) and figure of merit (ZT) at T = 300 K for both n/p-types of monolayers MoS2, MoSe2, and WS2 are in good agreement with the findings obtained by other models using the Boltzmann transport equation within a constant relaxation time framework.

Analysis of structural, electronic and optical properties of Er-doped rock salt AlN using ab-initio calculations.

This investigation includes the structural and optoelectronic characteristics of both pure and Er-doped rock salt aluminium nitride (AlN). Upon introducing Er doping into the AlN host, the calculations reveal a rise in the atomic parameter. Incorporating Er into the system leads to enhancements in the static dielectric coefficient ɛ1(0), static reflectivity R(0), as well as static refractive index n(0), at zero frequency. After doping, the peaks of imaginary dielectric tensor, extinction coefficient and absorption coefficient shift towards lower energy levels. Various exchange correlation potentials are incorporated to compare the results of electronic and optical characteristics. We employed the full potential linearized augmented plane wave (FP-LAPW) approach with WIEN2k code in conjunction with the density functional theory (DFT). To explore the optoelectronic characteristics of both pure as well as doped systems, three distinct exchange correlation potentials are utilized: the Perdew-Burke-Ernzerhof Generalized Gradient Approximation (PBE-GGA), Modified Becke Johnson Generalized Gradient Approximations (mBJ + GGA) and Hubbard potential (GGA + U).

Low-Energy Dipole Strength in 8\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^8$$\\end{document}He

In this work, we present new ab initio coupled-cluster calculations of dipole-excited state properties of 8\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^8$$\\end{document}He based on the chiral effective field theory interaction 1.8/2.0 (EM). We focus on the dipole polarizability, and compare the results to our previous study [Phys. Rev. C 105, 034313 (2022)] and subsequent theoretical work. With the aim of connecting the presence of low-lying dipole strength to structure properties of 8\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^8$$\\end{document}He, we compute the point-neutron radius, finding excellent agreement with available experimental data, and investigate its correlation with the dipole polarizability.

Pressure‐Driven Intrinsic Quantum Confinement and Semiconducting‐to‐Metallic Transition in the Topological Flat Bands Kagome Nb3Cl8 Compounds

AbstractNb3Cl8 is a unique subset of 2D crystalline materials renowned for their Kagome structure and distinctive flat energy bands. These bands contribute to the distinct electronic behavior, rendering Nb3Cl8 a compelling subject for study. In this study, by employing ab initio calculations, the impact of pressure on the electronic properties of Nb3Cl8is scrutinized, yielding valuable insights. Under high pressures, Nb3Cl8 undergoes a transition from a semiconductor state (with a 1.23 eV bandgap) to a metallic one, accompanied by electronic band restructuration. Notably, the flat energy bands are suppressed with increasing pressure. Furthermore, this investigation underscores the distinctive nature of flat energy bands in Nb3Cl8, delving into quantum effects, particularly their association with the quantum confinement of electronic states. The confinement of charge carriers in Nb3Cl8 results in discrete energy levels, corresponding to specific orbitals in the density of states, indicating robust electron confinement. Pressure‐induced changes in the energy gap between these quantized levels suggest a decrease in confinement strength. Consequently, the study lays a robust foundation for future exploration, contributing to the development of innovative electronic devices grounded in quantum confinement effects.

First principle calculations to explore the electronic, mechanical and optical properties of 2D NiX2 (X = O, S, Se) monolayers

This investigation employs ab-initio calculations to investigate the structural, dynamical, mechanical, and optoelectronic attributes of 1T-NiX2 (X = O, S, Se) monolayers. The confirmation of structural and dynamical stability is derived from negative cohesive energy values and the absence of negative frequencies in phonon dispersion spectra. Mechanical stability is established through the application of the Born-Huang stability criterion. Results indicate that an increase in the X-atom size from O to Se induces a reduction in material stiffness from 137.64 Nm−1 to 77.56 Nm−1 and thus, enhances the flexibility of the monolayers. The NiX2 monolayers exhibit indirect bandgap features with values 1.33 eV (1.81 eV), 0.63 eV (0.61 eV) and 0.28 eV (0.28 eV) using PBE (PBE+U) methods. Present results show an inverse relations between the band gap and the size of the X atom. The scanning tunnelling microscope (STM) images of 2D NiX2 monolayers are also simulated for experimental observations. Additionally, exploration of optical characteristics reveals high optical absorption (105 cm−1), which lies from infrared to UV-region. Moreover, NiO2 can be utilized as good wave anti-reflectors with reflection of incident light less than 7%. These results suggest NiX2 materials as promising candidates for diverse applications in optoelectronic and photovoltaic devices.

Low-index mesoscopic surface reconstructions of Au surfaces using Bayesian force fields

Metal surfaces have long been known to reconstruct, significantly influencing their structural and catalytic properties. Many key mechanistic aspects of these subtle transformations remain poorly understood due to limitations of previous simulation approaches. Using active learning of Bayesian machine-learned force fields trained from ab initio calculations, we enable large-scale molecular dynamics simulations to describe the thermodynamics and time evolution of the low-index mesoscopic surface reconstructions of Au (e.g., the Au(111)-‘Herringbone,’ Au(110)-(1 × 2)-‘Missing-Row,’ and Au(100)-‘Quasi-Hexagonal’ reconstructions). This capability yields direct atomistic understanding of the dynamic emergence of these surface states from their initial facets, providing previously inaccessible information such as nucleation kinetics and a complete mechanistic interpretation of reconstruction under the effects of strain and local deviations from the original stoichiometry. We successfully reproduce previous experimental observations of reconstructions on pristine surfaces and provide quantitative predictions of the emergence of spinodal decomposition and localized reconstruction in response to strain at non-ideal stoichiometries. A unified mechanistic explanation is presented of the kinetic and thermodynamic factors driving surface reconstruction. Furthermore, we study surface reconstructions on Au nanoparticles, where characteristic (111) and (100) reconstructions spontaneously appear on a variety of high-symmetry particle morphologies.

Transferable Anisotropic Mie Potential Force Field for Alkanediols.

The development of force fields for polyfunctional molecules, such as alkanediols, requires a careful account of different average intramolecular conformations for gas states compared to dense liquid states, where intra- and intermolecular hydrogen bonds compete. In the present work, the transferable anisotropic Mie (TAMie) potential is extended to 1,n-alkanediols. Using the convention that intramolecular nonbonded interactions up to and including the third neighbor are excluded, all force field parameters developed previously for 1-alcohols were transferred to 1,5-pentanediol and beyond, with good agreement with experimental phase equilibrium data. To obtain trans-gauche ratios of 1,2-ethanediol and 1,3-propanediol that are consistent with experimental results, the propensities for intra- and intermolecular hydrogen bonds had to be balanced. This was achieved by parameterizing the intramolecular dihedral energy functions governing the O-C-C-O and O-C-C-C angles while intramolecular charge-charge interactions were active. All partial charges belonging to a functional group are collected in a charge group and all interactions among two charge groups are evaluated even if they are separated by less than three bonds. With this approach, it is possible to apply the nonbonded parameters from 1-alcohols to alkanediols without further refinement. The agreement with experimental phase equilibrium and shear viscosity data is of similar quality as for the 1-alcohols and the trans-gauche ratio agrees with literature results from spectroscopic measurements and ab initio calculations.

Orientation-dependent deformation mechanisms of alpha-uranium single crystals under shock compression

Large-scale non-equilibrium molecular dynamics (NEMD) simulations were employed to investigate the dynamic deformations of alpha-uranium (α-U) single crystals subjected to varying shock strengths along low-index crystallographic orientations. The pronounced anisotropy of α-U gives rise to a complex microstructural evolution under shock loading. In-depth microstructural analysis of post-shock specimens reveals the identification of multiple dynamic deformation mechanisms. Notably, when the shock loading direction aligns with the a-axis, dynamic deformation of the α-U single crystals is primarily dominated by lattice instability, which attributes to a crystalline-to-amorphous transition serving as the dominant shear stress relaxation pathway. On the other hand, shock loading along the b-axis results in an abundance of deformation twins, with twinning planes identified as (130) and (13¯0). During the twinning event, the α-U matrix undergoes a transition to a metastable intermediate phase, subsequently decomposing into a composite structure comprising α-U twins and matrix. This unconventional twinning mechanism significantly deviates from classical theories. Furthermore, upon loading along the c-axis, twinning and a phase transition from α-U to body-centered tetragonal phase (bct-U) occur in α-U single crystal samples. Given that the pressure threshold of this phase transition predicted by ab initio calculations is as high as ∼270 GPa, the phase transition from α-U to bct-U might be implausible. An alternative interatomic potential of uranium with the higher pressure threshold was employed to reinvestigate the shock response of α-U single crystals along the c-axis. The phase transition of α-U to bct-U disappears, and twinning dominates the plastic deformation, with the twinning orientation conforming to the {112} twinning. The strong anisotropy of the α-U lattice triggers a wealth of orientation-dependent dynamic deformation mechanisms. The activation of the twinning system is evidently associated with the loading direction, constituting the potential cause for the discovery of multiple twinning variants during the deformation in polycrystalline uranium.

Interpretation of molecular electron transport in ab initio many-electron framework incorporating zero-point nuclear motion effects.

A computational methodology, founded on chemical concepts, is presented for interpreting the role of nuclear motion in the electron transport through single-molecule junctions (SMJ) using many-electron ab initio quantum chemical calculations. Within this approach the many-electron states of the system, computed at the SOS-ADC(2) level, are followed along the individual normal modes of the encapsulated molecules. The inspection of the changes in the partial charge distribution of the many-electron states allows the quantification of the electron transport and the estimation of transmission probabilities. This analysis improves the understanding of the relationship between internal motions and electron transport. Two SMJ model systems are studied for validation purposes, constructed from a conductor (BDA, benzene-1,4-diamine) and an insulator molecule (DABCO, 1,4-diazabicyclo[2.2.2]octane). The trends of the resulting transmission probabilities are in agreement with the experimental observations, demonstrating the capability of the approach to distinguish between conductor and insulator type systems, thereby offering a straightforward and cost-effective tool for such classifications via quantum chemical calculations.

Interatomic Potential For Carbon Based Quantum‐Technology Applications

AbstractTo optimize parameters for laser processing of quantum‐technology relevant materials, such as diamond, precise atomistic simulations of the light‐matter interaction on large scales (on the order of atoms) are essential. Classical empirical interatomic potentials are commonly employed for simulating such a large number of atoms, however they fail to accurately capture all relevant effects of light‐matter interaction. Conversely, ab initio methods like Density Functional Theory (DFT) can effectively incorporate quantum properties arising from photon excitations, but their applicability is limited to small systems containing at most approximately atoms. Consequently, bridging the gap between achieving DFT precision and handling millions of atoms necessitates the development of innovative classes of interatomic potentials. In this paper, the construction of a highly accurate interatomic potential for diamond is presented, derived from an extensive dataset of DFT calculations. The parameters of the interatomic potential depend on the electronic temperature (). The findings demonstrate that this newly developed interatomic potential can aptly describe the laser processing of diamond for nanophotonic applications, achieving accuracy comparable to ab initio methods for large systems.

Atomic scale mechanism of reorientation induced plasticity in titanium alloys - experimental and first principles investigation of the mobile [formula omitted] interfaces

Recent experiments identified a new type of stress induced structural transformation allowing to combine high strength, great work hardening and good ductility in multiphase Ti alloys. These properties are achieved through reorientation of the α′ martensite plates being in specific self accommodating 〈54‾1‾3〉 type II twin relation, i.e. under applied load one martensite variant reconfigure to its twinned configuration with visible motion of the {134‾1} twin boundary. This mechanism of plastic deformation was never observed before thus, its current understanding is fragmentary. In this article we present the results of experimental observations and ab initio calculations of 〈54‾1‾3〉 type II twins determining the crystallography of twin formation, structure and energy of the {134‾1} interface as well as mobility of the corresponding twinning disconnections. It was found that the investigated boundary has one of the lowest energies among known twinning modes in hexagonal Ti. Moreover, the 〈54‾1‾3〉{134‾1} disconnections have the smallest Burgers vector and step height in comparison to other active twinning systems. As a result, these disconnections are highly mobile which rationalize migration of the {134‾1} twin boundaries at straining. Furthermore, energy of the twin boundary and mobility of disconnections can be adjusted by particular alloying elements enabling the conscious development of new alloys exhibiting reorientation induced plasticity.

Spin-State Control in Dysprosium(III) Metallacrown Magnets via Thioacetal Modification.

Integrating controllable spin states into single-molecule magnets (SMMs) enables precise manipulation of magnetic interactions at a molecular level, but remains a synthetic challenge. Herein, we developed a 3d-4f metallacrown (MC) magnet [DyNi5(quinha)5(Clsal)2(py)8](ClO4)∙4H2O (H2quinha = quinaldichydroxamic acid, HClsal = 5-chlorosalicylaldehyde) wherein a square planar NiII is stabilized by chemical stacking. Thioacetal modification was employed via post-synthetic ligand substitutions and yielded [DyNi5(quinha)5(Clsaldt)2(py)8](ClO4)·3H2O (HClsaldt = 4-chloro-2-(1,3-dithiolan-2-yl)phenol). Thanks to the additional ligations of thioacetal onto the NiII site, coordination-induced spin state switching (CISSS) took place with spin state altering from low-spin S = 0 to high-spin S = 1. The synergy of CISSS effect and magnetic interactions results in distinct energy splitting and magnetic dynamics. Magnetic studies indicate prominent enhancement of reversal barrier from 57 cm-1 to 423 cm-1, along with hysteresis opening and an over 200-fold increment in coercive field at 2 K. Ab initio calculations provide deeper insights into the exchange models and rationalize the relaxation/tunnelling pathways. These results demonstrate here provide a fire-new perspective in modulating the magnetization relaxation via the incorporation of controllable spin states and magnetic interactions facilitated by the CISSS approach.

Spin‐State Control in Dysprosium(III) Metallacrown Magnets via Thioacetal Modification

Integrating controllable spin states into single‐molecule magnets (SMMs) enables precise manipulation of magnetic interactions at a molecular level, but remains a synthetic challenge. Herein, we developed a 3d‐4f metallacrown (MC) magnet [DyNi5(quinha)5(Clsal)2(py)8](ClO4)∙4H2O (H2quinha = quinaldichydroxamic acid, HClsal = 5‐chlorosalicylaldehyde) wherein a square planar NiII is stabilized by chemical stacking. Thioacetal modification was employed via post‐synthetic ligand substitutions and yielded [DyNi5(quinha)5(Clsaldt)2(py)8](ClO4)·3H2O (HClsaldt = 4‐chloro‐2‐(1,3‐dithiolan‐2‐yl)phenol). Thanks to the additional ligations of thioacetal onto the NiII site, coordination‐induced spin state switching (CISSS) took place with spin state altering from low‐spin S = 0 to high‐spin S = 1. The synergy of CISSS effect and magnetic interactions results in distinct energy splitting and magnetic dynamics. Magnetic studies indicate prominent enhancement of reversal barrier from 57 cm−1 to 423 cm−1, along with hysteresis opening and an over 200‐fold increment in coercive field at 2 K. Ab initio calculations provide deeper insights into the exchange models and rationalize the relaxation/tunnelling pathways. These results demonstrate here provide a fire‐new perspective in modulating the magnetization relaxation via the incorporation of controllable spin states and magnetic interactions facilitated by the CISSS approach.

Atomic force microscopy simulations for CO-functionalized tips with deep learning

Atomic force microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule is able to image the internal structure of molecules with an unprecedented resolution. The interpretation of these images is often difficult, making the support of theoretical simulations important. Current simulation methods, particularly the most accurate ones, require expertise and resources to perform ab initio calculations for the necessary inputs (i.e charge density and electrostatic potential of the molecule). Here, we propose a computationally inexpensive and fast alternative to the physical simulation of these AFM images based on a conditional generative adversarial network (CGAN), that avoids all force calculations, and uses as the only input a 2D ball–and–stick depiction of the molecule. We discuss the performance of the model when trained with different subsets extracted from the previously published QUAM-AFM database. Our CGAN reproduces accurately the intramolecular contrast observed in the simulated images for quasi–planar molecules, but has limitations for molecules with a substantial internal corrugation, due to the strictly 2D character of the input.

Defect Engineering for Enhanced Electrocatalytic Oxygen Reaction on Transition Metal Oxides: The Role of Metal Defects.

Metal defect engineering is a highly effective strategy for addressing the prevalent high overpotential issues associated with transition metal oxides functioning as dual-function commercial oxygen reduction reaction/oxygen evolution reaction catalysts for increasing their activity and stability. However, the high formation energy of metal defects poses a challenge to the development of strategies to precisely control the selectivity during metal defect formation. Here, density functional theory calculations are used to demonstrate that altering the pathway of metal defect formation releases metal atoms as metal chlorides, which effectively reduces the formation energy of defects. The metal defects on the monometallic metal oxide surface (Mn, Fe, Co, and Ni) are selectively produced using chlorine plasma. The characterization and density functional theory calculations reveal that catalytic activity is enhanced owing to electronic delocalization induced by metal defects, which reduces the theoretical overpotential. Notably, ab initio molecular dynamics calculations, ex situ XPS, and in situ ATR-SEIRAS suggest that metal defects effectively improve the adsorption of reactive species on active sites and enhance the efficiency of product desorption, thereby boosting catalytic performance.