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Electron correlation by exchange mapping in electronic structure calculations
A method for increasing the accuracy of configuration interaction (CI) calculations of molecules and other electronic systems is proposed. The energy defect of a given calculation is associated with the electron pair origin of configurations not yet generated, and this defect is mapped onto the exchange interaction for the corresponding pair of spatial molecular orbitals. The orbitals can have opposite spins, and thus, the contribution includes the self-energy and differs from fermion exchange due to antisymmetry. A single parameter, γ, multiplying the exchange integral, is determined from the exact thermodynamic energy of a few reference molecules. The value of γ depends on the basis and level of configuration interaction but is the same for all molecules. Calculated energies are compared with experimental thermodynamic data for a set of forty mainly organic molecules, representing a wide range of bonding environments. Results are reported for two types of multi-reference CI calculations: (1) a triple-zeta basis plus d-type functions for C, N, O, and F and an s, p basis for H, and (2) a severely truncated virtual space in which higher spherical harmonic basis functions are removed. The error of the initial CI calculations is large; however, including the exchange-based contribution brings calculated CI energies into much closer agreement with exact values.
Explicit particle kinetics simulations of reactive diffusion at air–water interfaces
Reactive uptake of trace gases by aqueous aerosols reflects a balance between molecular diffusion and chemical reaction, yet separating interfacial from bulk contributions remains challenging. We present an explicit particle-based reactive diffusion framework that directly simulates stochastic transport and reactions at air–water interfaces. Using ozone–nitrite (O3−NO2−) as a model system, we show that concentration profiles reproduce the reacto-diffusive theory, allowing quantitative extraction of the characteristic length. The framework further resolves interfacial vs bulk reactivity, revealing that interfacial chemistry dominates when droplet radii approach or fall below the reacto-diffusive length. The results are presented for the well-established ozone–nitrite chemistry as a test case. Molecular encounters remain within the single-molecule limit, ensuring relevance to atmospheric conditions at lower concentrations without loss of generality. This framework provides a rigorous means to mechanistically connect microscopic kinetics with macroscopic uptake and is readily extendable to multiphase systems. This study further highlights the need for simulation frameworks to resolve nanometer-scale interfacial regions when droplet sizes approach the reacto-diffusive length, where the transition from diffusion-limited to reaction-limited behavior in bulk liquid elevates the dominance of interfacial chemistry.
Electrostatic slowdown in kinetics of spinodal decomposition
We consider the kinetics of spinodal decomposition in a mixture of oppositely charged ionic species A− and C+ with a short-range Flory–Huggins incompatibility, χ > 0, between them. This represents the minimal model of systems with short-range attractions and long-range repulsions. In contrast to nonionic blends undergoing macroscopic phase separation, ionic mixtures at equilibrium form periodic phases of finite-size domains or clusters—a phenomenon known as electrostatically stabilized microphase separation. A dynamical (time-dependent Ginzburg–Landau) field theory is developed, classified as Model B plus long-range Coulomb interactions. Electrostatics generates an extra term in the resulting Cahn–Hilliard equation, which slows spinodal decomposition. Analysis of the amplification factor R(q) in the Fourier domain shows that electrostatic interactions (i) do not affect the optimal wavevector qm; (ii) slow down the optimal growth; (iii) reduce the window of positive growth, R(q) > 0, by suppressing long-wavelength modes due to the high Coulomb cost of large charged domains; and (iv) lead to a new critical scaling of the optimal growth rate with quench depth, Ropt ∼ δχ1, contrasting the exponent 2 for nonionic systems. Extension to polymer blends shows that monomer connectivity and Rouse dynamics shift qm to lower values and further decelerate growth. In dimensionless form, R(q/qm) depends on two parameters: the reduced electrostatic strength, linear in the Bjerrum length, and the reduced chain length. After rapid spinodal decay, clusters slowly coarsen to their equilibrium finite size, which exceeds the spinodal pattern scale. These results advance the understanding of the dynamics of biocondensate formation in living cells, where Coulomb interactions are ubiquitous.
Photoelectron spectroscopy and structural characterization of [EDTA · M(II)]2− · <i>n</i> H2O (M = Ni, Cu, Zn; <i>n</i> = 0–2) complexes
We investigated microhydrated transition metal-ethylenediaminetetraacetic acid (EDTA) dianion complexes [EDTA · M(II)]2− · nH2O (M = Ni, Cu, and Zn; n = 1, 2) using cryogenic photoelectron spectroscopy in conjunction with theoretical calculations. The measured spectra of [EDTA · Ni/Zn(II)]2− · nH2O closely resemble those of their corresponding bare dianions, with a systematic shift toward the high electron binding energy side upon stepwise hydration and featuring a hexadentate metal-EDTA binding motif. In contrast, the spectra of hydrated [EDTA · Cu(II)]2− exhibit broadened first detachment bands, implying the coexistence of multiple metal–ligand binding forms, as a consequence of the Jahn–Teller effect associated with its d9 electron arrangement. These findings showcase molecular-level insights into the structural adaptability of EDTA-based supramolecular assemblies comprising transition metal ions, water molecules, and multidentate ligand environments.
Achieving all-atom molecular dynamics accuracy from the Poisson–Boltzmann method through machine learning
All-atom molecular dynamics (MD) simulations are a standard tool for probing the structural and dynamical properties of biomolecular systems, but their accuracy comes at the cost of high computational demands. To overcome spatial–temporal limitations, implicit models or coarse-graining are often employed, but usually at the expense of reduced accuracy. This limitation is also evident in the Poisson–Boltzmann (PB) mean-field theory, which efficiently captures long-range electrostatics but fails to account for crucial short-range interactions. In this work, we bridge this gap by introducing a graph neural network (GNN) Δ-learning approach trained on the difference between all-atom MD and PB, resulting in DIS-PB (deep implicit solvation model using the PB potential as a prior). DIS-PB, which models solutes and salt ions explicitly by MD while water is coarse-grained out, captures both short-range electrostatic correlations as well as long-range electrostatic interaction tails. Applied to a system of the DNA molecule in 1 mol l−1 salt solution, our method reproduces structural properties (NDPs, RDFs, and binding probability patterns) with high fidelity, showing that the GNN-corrected PB can reach the accuracy of all-atom MD at a lower computational cost.
Siam Quantum 2: An open-source C toolbox for quantum modeling and electronic structure development
We present Siam Quantum 2, the next generation of the open-source C program originally published in 2012 for Hartree–Fock electronic structure calculations [T. Khamla and T. Chachiyo, KKU Research Journal (Graduate Studies) 12(3), 8–28 (2012)], developed in Thailand (historically known as Siam) as a platform for quantum chemistry research and education. Over the past decade, Siam Quantum has evolved into a modular toolbox supporting a wide range of quantum modeling capabilities, including density functional theory, second-order Møller–Plesset perturbation theory, analytic energy gradients, molecular geometry optimization, quantum molecular dynamics, and minimum energy crossing point search. The present version introduces an extensible C architecture designed for method development, readability, and performance on multi-CPU environments. Each computational module is accompanied by human-readable Markdown documentation that contains LaTeX-style equations and programming guides, bridging the theoretical formulation and source code and facilitating future computational development. This paper describes the program’s design philosophy, theoretical framework, and implementation details. We also highlight studies by various research groups that have made use of Siam Quantum, illustrating how the software can be used for quantum modeling and electronic structure studies.
Dissociation behavior of hydrogen bromide dications investigated using multielectron–ion coincidence spectroscopy
The dissociation behavior of hydrogen bromide dications (HBr2+) produced by the Auger decay of Br 3d core-hole states in HBr was investigated using multielectron–ion coincidence spectroscopy. Coincidence detection of 3d photoelectrons, the associated Auger electrons, and ions was conducted to identify the metastability and dissociation pathways of individual electronic states in the dications. Vibration levels v = 0–3 of the X3Σ− ground state and v = 0 of the a1Δ state survive beyond 10 μs, whereas the v ≥ 1 level of the a1Δ state exhibits predissociation on the submicrosecond timescale. Higher electronic states promptly dissociate into H+ + Br+ or H + Br2+ fragments.
Improved molecular conductance predictions using wavefunction-in-DFT quantum embedding
A novel electronic structure methodology to describe electron transport in single-molecule junctions (SMJs) within non-equilibrium Green’s function theory is presented. The approach is based on a formally exact, projection-based quantum embedding technique that combines correlated many-electron wavefunction models for the molecular region with a density functional theory (DFT) description of the metallic electrodes. This is achieved by constructing a specialized Hamiltonian for the molecular domain, leveraging Dyson orbitals corresponding to the ionized and electron-attached states of the embedded molecule. The effectiveness of this wavefunction-in-DFT embedding scheme is demonstrated through transport calculations for SMJs containing benzene-1,4-diamine and its substituted derivatives, employing Hartree–Fock, SOS-ADC(2), and CCSD methods for the molecular subsystem. The results show a marked improvement in the predicted zero-bias conductance compared to conventional DFT-based transport modeling employing the PBE functional. The proposed methodology provides a systematic way to select the most suitable electronic structure methods for the different parts of the system, maintaining a balance between accuracy and computational cost, while ensuring a proper description of electronic correlation within the molecule, which may notably impact electron transport in certain systems.
Microscopic structure of aqueous alkylamine mixtures: A computer simulation study
We examine the microscopic origin of the pronounced x-ray scattering pre-peaks observed in water-rich aqueous alkylamine mixtures. While neat amines display weak pre-peaks compared to alcohols, and aqueous alcohols generally exhibit none, aqueous amines display a striking and unexpected signal. Molecular dynamics simulations of primary amines from propylamine to octylamine show that nitrogen head groups preferentially saturate the surfaces of water-rich domains, stabilizing both water and amine regions through water–nitrogen donor hydrogen bonding. This interfacial anchoring prevents macroscopic demixing except at high water contents, where too few amines remain to cover the interfaces. The resulting disordered bilayer-like arrangement generates long-ranged domain oscillations that appear as positive like–like species and negative cross species correlations, whose partial cancellation produces the experimental pre-peak. Model comparisons further show that the effect is highly sensitive to both solute and water force fields, with the CHARMM-AA/SPC/E combination offering the most consistent description. These results establish aqueous amines as prototypical systems in which stable micro-heterogeneity and supramolecular topology directly give rise to scattering pre-peaks, providing a concrete bridge between molecular liquids and micro-emulsions.
Observation of laser-assisted elastic electron scattering by Ar in circularly polarized femtosecond laser fields
Laser-assisted electron scattering (LAES) by argon atoms driven by circularly polarized femtosecond near-infrared laser fields was studied using 1 keV electrons in the single-collision regime. Energy- and angle-resolved LAES signals were recorded with an angle-resolved time-of-flight spectrometer. A direct comparison of experimental results using linear, left-circular, and right-circular polarized lasers revealed a systematic decrease in LAES intensity under circular polarization. Numerical simulations based on Mittleman’s extension of the Kroll–Watson theory reproduced the observed polarization dependence in both energy and angular distributions. No significant difference was found between left- and right-circular polarization within experimental uncertainty, in line with the theoretical prediction that the helicity-dependent contribution is negligible compared to the main term. These agreements confirm that the measured behavior is consistent with Mittleman’s theory.
From delocalized orbitals to Lewis structures: Trade-offs in the imperfect art of chemical bonding analysis
Orbital-based bonding analysis has become an essential component of structure and bonding studies in chemistry. However, the proliferation of bonding analysis tools has led to an overwhelming variety of results presented in many application studies, often lacking a clear framework for interpretation. In this work, we critically examine the desirable features of these analysis tools and explore the inherent limitations that prevent a single tool from satisfying all criteria. By discussing the trade-offs commonly encountered in bonding analysis, we aim to provide insights that will guide the future development and selection of more effective analysis tools.
Density functional theory study on the reaction mechanism of 1-nitroanthraquinone synthesis by nitration of anthraquinone mixed acid
The nitration of anthraquinone (AQ) to form 1-nitroanthraquinone (1-NAQ) is a key step of significant industrial value in aromatic nitration reactions. However, its microscopic mechanism and the formation mechanism of regioselectivity have long lacked clear theoretical explanations. This study employs density functional theory calculations combined with an implicit solvent model to reveal the complete reaction pathway of AQ nitration under mixed acid conditions at the atomic scale. Both kinetic and thermodynamic results consistently indicate that this reaction follows a typical two-step electrophilic aromatic substitution mechanism: the attack of the nitroyl ion (NO2+) on the C1 site constitutes the rate-determining step (energy barrier: 7.327 kcal/mol), while the sulfite ion abstracts the intermediate H to form 1-NAQ (energy barrier: 2.896 kcal/mol). The highly regional selectivity of the reaction toward C1 is elucidated through the local electronic structure characteristics, charge distribution, and the formation and cleavage behavior of key bonds. Thermodynamic analysis further reveals that the Gibbs free energy of both transition states decreases significantly with increasing temperature, reflecting strong thermal driving forces. The variation in heat capacity with temperature indicates the electronic restructuring accompanying the destruction and restoration of aromaticity during the reaction process. This study elucidates the mixed-acid nitration reaction mechanism of AQs, providing a comprehensive quantitative description of the nitration mechanism for AQ compounds. It establishes a theoretical foundation for designing safe, efficient, and continuous nitration processes.
Quantum chemical analysis of the conformers, fundamental vibrational frequencies, and spectroscopic constants of methanetriol
The recent synthesis of methanetriol [CH(OH)3] under simulated interstellar conditions implies that this molecule may be present in various astronomical environments. This explicitly correlated coupled cluster theory study highlights that of the three conformers, the lowest-energy C1 form is polar enough (1.51 D) and exhibits unique enough rotational constants predicted in this work, such that its observation is possible. Furthermore, the IR spectrum of the next-highest-energy conformer, Cs, will likely overlap with that of C1 for its unique molecular vibrations, but the highest-energy C3 conformer may be distinguishable in the IR, especially for its C–H stretch at 2889.2 cm−1. All three conformers exhibit strong C–O stretching features around 1000 cm−1 and notable hydride bends between 1400 and 1500 cm−1. Sterics appear to be stronger factors than the intramolecular hydrogen bonding in terms of the relative energies for the three conformers. Hybrid quartic force fields treat the low frequency fundamentals more reliably than pure, composite methods.
Performances of simplified models of cyanocobalamin for first-principles calculations
Cyanocobalamin (CNCbl) is a key member of the family of organometallic molecular catalysts. Consequently, both experimental and theoretical investigations of CNCbl are essential for advancing the fundamental understanding of its structural and catalytic properties. However, the inherent complexity of its molecular architecture poses significant challenges for theoretical studies. To address this, several studies have employed simplified structural models of CNCbl. In the present work, we systematically investigate the structural, electronic, and magnetic properties of various reduced CNCbl models, alongside the complete CNCbl molecule, using density functional theory. Our results reveal that the electronic structure, magnetic behavior, and oxidation state undergo substantial modifications in the reduced models compared to the full CNCbl system. In particular, the complete CNCbl structure exhibits a non-magnetic semiconducting character with a +3 oxidation state of the Co center, whereas the overly simplified models display magnetic behavior with a +2 oxidation state. These pronounced changes in oxidation and magnetic character also lead to significant alterations in catalytic properties. The influence of these effects is further demonstrated through Cl adsorption studies. In the full CNCbl model, Cl binds strongly at the Co site, while in the reduced models, the interaction becomes considerably weaker. These findings underscore that, despite advances in computational resources, the use of oversimplified CNCbl models can yield misleading predictions. Therefore, the complete CNCbl structure should be preferred for reliable theoretical investigations of both its fundamental and catalytic behavior.
Non-equilibrium charge transport through molecular junctions as stochastic many-electron dynamics
To study time-resolved electric currents through molecular electronic systems, it is common to use real-time time-dependent functional theory, non-equilibrium Green’s function, or the driven Liouville–von Neumann method, among others. These approaches are based either on the one-electron density or on the one-electron density matrix theory, and attempts to treat electron transport from a many-electron perspective are few and far apart. In this contribution, we take the first step toward describing charge transport through a molecular nanojunction as a stochastic many-electron dynamics treated as a piecewise deterministic process. Stochastic methods have previously been employed to describe various electrodynamical processes. Here, we employ an open-system time-dependent configuration interaction ansatz with a resolution-of-identity Hamiltonian to describe the motion of electrons and holes through the nanojunction subject to interaction with open boundary conditions. The absorption of charge carriers into reservoir states is described using Lindblad operators to simulate the conductance behavior in real time. Incoming charge carriers are described as bias-dependent excitations that create electron–hole pairs localized at the junction. To test the method, we use a quinone/hydroquinone nanojunction as a toy problem, exhibiting a marked change in conduction due to quantum interferences.
Remarkable performance of triatomic single-cluster catalyst of Ti3@graphdiyne in electrocatalytic nitrogen reduction
The electrocatalytic nitrogen reduction reaction offers a sustainable route for unconventional ammonia synthesis, yet its practical implementation is often hindered by catalyst performance. Herein, by using first-principles calculations, we systematically explore the eNRR performance of a series of single-cluster catalysts with monometallic triatomic clusters of 3d transition metals anchored on graphdiyne (TM3/GDY, TM = Sc–Zn). The Ti3/GDY, V3/GDY, Cr3/GDY, and Mn3/GDY all exhibit robust stability and feature spontaneous N2 chemisorption and significant N≡N bond activation (elongation &gt; 0.14 Å). Chemical bonding analysis uncovers σ–π synergistic donor–acceptor interactions between TM-3d orbitals and N2 π* antibonding states as the origin of superior catalytic activity. Ti3/GDY achieves a low limiting potential of −0.39 V while effectively suppressing N2H4 formation. This dual advantage stems from its elevated d-band center and high charge transfer. The titanium-based triatomic architecture is found to be a promising candidate for sustainable nitrogen fixation. This work offers a fundamental design principle for SCCs through atomic-level coordination engineering and electronic structure modulation.
Harmonic-to-anharmonic thermodynamic integration made simple using REG TI
Standard harmonic-to-anharmonic thermodynamic integration (TI) is known to develop a near singularity in the integrand for solids exhibiting diffusive degrees of freedom, such as rotating functional groups or migrating defects. This pathology results in numerical challenges for estimating absolute free energies within a single thermodynamic cycle. In this work, we introduce a simple regularization that removes this singularity and yields a well-behaved integrand that can be accurately evaluated on a uniform grid. The approach—termed Regularized End point Gradient (REG) TI—is demonstrated on a model system and on predicting the relative stability of paracetamol polymorphs for which quasi-free methyl rotations lead to a near singularity in standard TI. We expect REG TI to simplify anharmonic free energy calculations for solids and to potentially enable their automation.
Atomic-scale insights into the dual-functional catalytic mechanism of Pd clusters on crystalline carbon nitride
The rational design of efficient bifunctional catalysts for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) is crucial for advancing sustainable energy conversion technologies. In this study, spin-polarized density functional theory calculations were performed to systematically investigate palladium (Pd) clusters of different sizes (n = 1–10, 13) supported on the PTI/Li+Cl− (100) surface, which is the oxidation site in experiments. Strong metal–support interactions were found to effectively stabilize Pd clusters on PTI, ensuring robust structural integrity. Free-energy analyses reveal a distinct size-dependent catalytic behavior, with Pd4@PTI exhibiting the lowest overpotentials for OER (0.41 V) and ORR (0.95 V). Further examination of scaling relations, free-energy profiles, and electronic descriptors demonstrates that the superior performance of Pd4@PTI originates from a balanced adsorption strength of oxygen intermediates, modulated by electronic interactions between Pd clusters and the PTI substrate. These findings provide fundamental insights into the size-dependent activity of Pd clusters on PTI and offer theoretical guidance for the rational design of cost-effective and durable Pd-based catalysts for clean energy applications.
Probing the gold–hydrogen analogy in [L–Au–SR]− complexes (L = H and Au; R = H and CH3)
Thiolate-protected noble-metal clusters play essential roles in numerous applications, rendering this area one of the most vibrant research frontiers. The gold–hydrogen analogy has been firmly established in various hydrogen-atom-doped small gold clusters. In this work, we systematically investigate the chemical bonding characteristics in isolated model systems of [L–Au–SR]− (L = H and Au; R = H and CH3) complexes. By combining gas-phase negative ion photoelectron velocity-map imaging (NI-PEVMI) with density functional theory calculations, we demonstrate that the geometric and frontier molecular orbital properties of Au2SR− (R = H and CH3) closely mimic those of HAuSR− (R = H and CH3), respectively. Furthermore, our analyses reveal that the covalent character of the bonds is ligand-dependent and follows the trend: Au–H &gt; Au–Au &gt; Au–S.
Performance comparison of slit and nanoporous graphene oxide membranes in water desalination
Graphene oxide (GO) membranes have emerged as promising candidates for water desalination as a result of their structural and transport properties. In this study, we employ fully atomistic classical molecular dynamics simulations to investigate the performance of monolayer GO membranes featuring pore- and slit-like nanostructures. We analyze the influence of the width of the slits, ranging from 0.8 to 1.5 nm, on water transport and salt rejection by monitoring the spatial and temporal distributions of water molecules and ions. Furthermore, we assess the effect of applied pressure on water density profiles and compute the potential of mean force for water molecules traversing the slits. Our results reveal that slits offer tunable transport characteristics and that nanopores generally outperform slits in the combined metrics of water flux and ion exclusion at low pressures. At higher pressures, however, 1.0–1.5 nm slits exhibit a permeability gain that can exceed comparable nanopore systems, with a reduction in salt rejection, whereas 0.8 nm slits retain near-complete ion exclusion over the range examined. These findings delineate operating regimes in which each architecture is advantageous and guide the optimization of nanostructure design for advanced desalination technologies.