Ab Initio Calculations Research Articles

Quantum study of the CH3+ photodissociation in full-dimensional neural network potential energy surfaces.

C H 3 + , a cornerstone intermediate in interstellar chemistry, has recently been detected for the first time by using the James Webb Space Telescope. The photodissociation of this ion is studied here. Accurate explicitly correlated multi-reference configuration interaction abinitio calculations are done, and full-dimensional potential energy surfaces are developed for the three lower electronic states, with a fundamental invariant neural network method. The photodissociation cross section is calculated using a full-dimensional quantum wave packet method in heliocentric Radau coordinates. The wave packet is represented in angular and radial grids, allowing us to reduce the number of points physically accessible, requiring to push up the spurious states appearing when evaluating the angular kinetic terms, through projection technique. The photodissociation spectra, when employed in astrochemical models to simulate the conditions of the Orion bar, result in a lesser destruction of CH3+ compared to that obtained when utilizing the recommended values in the kinetic database for astrochemistry.

Unifying O(3) Equivariant Neural Networks Design with Tensor-Network Formalism

Abstract Many learning tasks, including learning potential energy surfaces from ab initio calculations, involve global spatial symmetries and permutational symmetry between atoms or general particles. Equivariant graph neural networks are a standard approach to such problems, with one of the most successful methods employing tensor products between various tensors that transform under the spatial group. However, as the number of different tensors and the complexity of relationships between them increase, maintaining parsimony and equivariance becomes increasingly challenging. In this paper, we propose using fusion diagrams, a technique widely employed in simulating SU($2$)-symmetric quantum many-body problems, to design new equivariant components for equivariant neural networks. This results in a diagrammatic approach to constructing novel neural network architectures. When applied to particles within a given local neighborhood, the resulting components, which we term "fusion blocks," serve as universal approximators of any continuous equivariant function defined on the neighborhood. We incorporate a fusion block into pre-existing equivariant architectures (Cormorant and MACE), leading to improved performance with fewer parameters on a range of challenging chemical problems. Furthermore, we apply group-equivariant neural networks to study non-adiabatic molecular dynamics of stilbene cis-trans isomerization and water adsorption cycles in porous materials, such as metal-organic frameworks. Our approach, which combines tensor networks with equivariant neural networks, suggests a potentially fruitful direction for designing more expressive equivariant neural networks.

Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer.

We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.

Solvent Effects on the Absorption and Emission Spectra of the [5-amino-1-bromoindolizin-3-yl](4-bromophenyl)methanone Molecule.

The effects of solvent on the absorption and emission spectra and dipole moments of the 5ABBM have been extensively studied in a series of solvents. The dipole moments in the excited state are observed to be greater than those in the ground-state in all the solvents studied for the chosen molecule. The dipole moment increase in the excited singlet state ranges from 2.42 to 24.14 D. The experimentally calculated ground state and excited state dipole moments were determined using the solvatochromatic shifts in the absorption and emission spectra as a function of dielectric constant (ɛ) and refractive index (n). These data are used to estimate the excited-state dipole moment using the experimentally determined ground-state dipole moment. A series of fifteen different organic solvents (toluene, methanol, n-butyl alcohol, ethyl acetate, DMS, acetonitrile, benzene, isopropyl alcohol, water, DMF, DCM, DIO, THF, ethanol, and octanol) were investigated at constant dye concentrations. Small changes in the fluorescence spectrum were observed for the different solvents; the highest fluorescence intensity was observed for DMS, and the lowest was observed for water. The Stokes shift in different solvents was studied for the 5ABBM molecule. This results in molecule being more polar in the excited state than in the ground state for the solvents used. The ground state dipole moments, HOMO-LUMO, and molecular electrostatic potential maps were also computed via ab initio calculations and evaluated via Gaussian 09W software.

Coherence mapping to identify the intermediates of multi-channel dissociative ionization

Identifying the short-lived intermediates and reaction mechanisms of multi-channel radical cation fragmentation processes remains a current and important challenge to understanding and predicting mass spectra. We find that coherent oscillations in the femtosecond time-dependent yields of several product ions following ultrafast strong-field ionization represent spectroscopic signatures that elucidate their mechanism of formation and identify the intermediate(s) they originate from. Experiments on endo-dicyclopentadiene show that vibrational frequencies from various intermediates are mapped onto their resulting products. Aided by ab initio methods, we identify the vibrational modes of both the cleaved and intact molecular ion intermediates. These results confirm stepwise and concerted fragmentation pathways of the dicyclopentadiene ion. This study highlights the power of tracking the femtosecond dynamics of all product ions simultaneously and sheds further light onto one of the fundamental reaction mechanisms in mass spectrometry, the retro-Diels Alder reaction.

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.

Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation

In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using “Atom in molecules” (AIM), “Natural Bond Orbital” (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.

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.

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.

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production.

Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.

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.