Journal of Chemical Physics最新文献

The nudged elastic band (NEB) method is a widely used algorithm for determining minimum energy paths and transition states in chemical reactions and phase transitions. In this work, we present the implementation of different NEB algorithm schemes in the CRYSTAL code, a quantum mechanical ab initio program for the calculation of electronic properties of condensed matter systems, based on Hartree-Fock and density functional theory. The use of a set of localized Gaussian-type functions to expand the wavefunction permits a very efficient evaluation of the exact exchange series for the hybrid exchange-correlation functionals. Therefore, our implementation allows an accurate characterization of transition states in both molecular and condensed phase systems, at the hybrid functional level of theory. The theoretical framework, including the force projection scheme, tangent estimation, optimization strategies, as well as the extensions of the method with climbing image and variable spring constants variants, is recalled. Then, the NEB algorithm is validated through a series of benchmark tests: two molecular reactions (a collinear proton transfer process and the keto-enol tautomerization in formamide) and a proton exchange process in a periodic chabazite zeolite. Our results are in excellent agreement with experimental and previous theoretical data, confirming the accuracy and applicability of the implementation. This work opens the possibility for future studies of complex reactive processes on extended periodic systems, using hybrid functionals.

An accurate description of target molecular orbitals is essential for modeling the electron-molecule scattering process. Here, we devise a framework for optimizing target molecular orbitals by numbering and weighting state-averaged molecular configuration wave functions automatically according to the experimental parameters to investigate low-energy electron scattering from carbon monoxide using the ab initio R-matrix method. Its main feature is the ability to provide optimal target molecular orbitals in terms of various specific elastic and inelastic scattering processes. Agreement with the available measurements and previous calculations is mostly excellent. The good description of the electronic dipole moment for the CO molecule plays a key role in determining the rotational excitation and elastic scattering results. The electronic excitation energies contribute to the accuracy of electronic excitation cross sections, with a low root-mean-square error of only 0.06 Å2. This study may pave a promising pathway for enhancing the study of electron-molecule scattering.

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born-Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree-Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

Ionic liquid-iron porphyrin (IL-FeP) complexes are systems with diverse applications, particularly in oxygen reduction reactions and the biodegradation of ionic liquids by cytochrome P450 enzymes, where FeP serves as the active site. Despite the importance of such systems, there is currently a lack of information on the conformational preference of ionic liquids binding to FeP and the influence that such binding conformations exert on the electronic properties of FeP. In addition, the role of binding interactions in facilitating biodegradation of ionic liquids is not yet fully understood. In this article, we address the knowledge gap by employing density functional theory calculations to identify the most stable structures of IL-FeP complexes. We considered four ionic liquids containing the cation 1-hexyl-3-methylimidazolium paired with acetate, methanesulfonate, ethylsulfate, and butylsulfate anions. Thermodynamic analysis of binding was supplemented with energy decomposition analysis, non-covalent interaction analysis, and natural bond orbital analysis to glean insight into the energetic factors driving binding stability. Our results reveal conformations in which one of the oxygen atoms in the anions is positioned directly above Fe, and the imidazolium ring aligns approximately parallel to the FeP plane, which are characterized by strong binding energies, irrespective of the organic anion involved. Electrostatic interactions between the IL ions and FeP play a dominant role in determining the binding conformations. The propensity to acquire an electron by an IL-FeP complex is significantly reduced when oxygen in the anion is in close proximity to Fe. These findings enhance our understanding of the fundamental interactions governing IL-FeP complexes, providing a foundation for tailoring ionic liquids for specific applications in catalysis and biodegradation.

Chiral Induced Spin Selectivity (CISS) is an intriguing phenomenon in chiral molecules, in which spin polarization emerges at room temperature in two-terminal junctions without requiring ferromagnetic contacts or strong intrinsic spin-orbit coupling. This work develops a unified tight-binding framework that reproduces charge and spin transport in single- and double-helical molecules, including ordered oligopeptides and DNA. We first reproduce the spin-independent conductance-distance behavior observed by Giese, Curr. Opin. Chem. Biol. 6, 612 (2002), and Lindsay, Life 10, 72 (2020), by including electron-phonon interactions through Einstein phonon reservoirs at temperature T. Upon introducing spin-orbit coupling under the tunneling barrier for single-stranded DNA, we obtain a clear spin-conductance asymmetry, leading to strong spin polarization (20%-40%) that increases with molecular length and reverses sign with molecular chirality. The temperature dependence of the polarization exhibits a linear increase near room temperature, consistent with experimental trends. Double-stranded configurations yield similar spin-selective behavior within the experimental setup. We argue that this class of models provides the closest microscopic correspondence to current CISS measurements and that further refinements can be achieved by identifying specific decoherence processes and barrier parameters associated with each molecular system.

The complex between pyrazole and carbon dioxide has been generated in a supersonic jet and characterized using Fourier transform microwave spectroscopy and state of the art CCSD(T) theoretical calculations. The complex presents a planar configuration showing a simultaneous N⋯C=O n → π* tetrel bond and a NH⋯O hydrogen bond. The TS internal rotation barrier that interconverts the oxygen atoms of CO2 has been calculated to be 10 kJ mol-1 at the CCSD(T) level. The electronic characteristics of the minimum and TS have been analyzed. Machine learning methods have been applied to predict the potential energy surface of the pyrazole⋯carbon dioxide complex.

Aqueous zinc-ion hybrid capacitors (ZIHCs) have garnered significant attention due to their cost-effectiveness, safety, and high theoretical capacity. However, the use of carbon-based materials in ZIHCs faces challenges such as electrolyte ion and pore size mismatching, inadequate infiltration between electrolyte and electrode, and limited surface active sites and defects, all of which impede the device's ability to achieve optimal energy density and electrochemical performance. To address these issues, a three-dimensional N and O co-doping hierarchical porous activated carbon (3DNOHC) with an ultrahigh specific surface area of 3477.69 m2 g-1 is synthesized through the direct calcination of nitrilotriacetic acid sodium salt precursor followed by a chemical activation process. Density functional theory calculations demonstrate that the N/O co-doping of activated carbon significantly enhances the ion adsorption/desorption capabilities on the surface of the materials, thereby improving their kinetic and electrochemical properties. The structural changes in zinc metal anodes and 3DNOHC cathodes during charging/discharging are investigated using ex situ XRD and ex situ Raman tests. Due to its abundant porous structure and active sites, the 3DNOHC-6 sample exhibits rapid ion transport and impressive electrochemical performance in ZIHCs. In particular, the 3DNOHC-6//Zn device demonstrates a high reversible capacity of 171/102 mA h g-1 at 0.2/10 A g-1 and an outstanding energy density of 137 Wh kg-1@160 W kg-1. Moreover, it exhibits excellent capacity retention of 80% at 5 A g-1 after 45 000 cycles. This study serves as a valuable reference for the development of activated carbon cathode materials for aqueous hybrid capacitors aiming for high energy/power density.

In this work, we present a hierarchical approach to generate ferroelectric covalent frameworks based on rotatable polar groups. By using a multi-step workflow of increasing theoretical sophistication but also increasing computational costs, a unit cell with ferroelectric behavior can be generated for a given organic linker group. Starting with a basic point dipole model to find an appropriate unit cell, followed by a three-dimensional representation of the organic rotor, up to the full framework, each step confirms the desired attributes. This is achieved by using molecular dynamics and Monte Carlo Metropolis sampling in combination with the "Universal Force Field for Metall-Organic-Frameworks" (UFF4MOF) and the van der Waals corrected density functional tight-binding approach (known as GFN1-xTB) for the energy calculations. As a result, we demonstrate a covalent organic framework that is predicted to show a ferroelectric ground state that is stable up to temperatures beyond 100 K.

Ultrafast pump-probe time resolved x-ray spectroscopy carries information on the valence-core dynamics of molecular systems. Here, a coherent two-dimensional nonlinear electronic-x-ray spectroscopy (2DEX) application is proposed in order to reveal the frequency-frequency correlations for the valence and the core transition excitations. 2DEX is in the class of extreme-cross peak correlation spectroscopy and is experimentally straightforward to measure as an adaptation of the conventional optical pump-x-ray probe technique by creating a phase-locked pulse pair of the ultrafast laser for the valence excitation. Theoretical evaluation of the coherences and populations for several applications of ultrafast valence-core spectroscopy experiments is shown. Using a response function approach, 2DEX, four wave signals are calculated and evaluated with respect to frequency separation in the electronic and x-ray ranges as well as the line shape characteristics. It is shown that stationary and oscillatory contributions to the rephasing, non-rephasing, and absorptive signals can be resolved depending on pulse shaping and phase cycling, phase matching, x-ray spectrometer, and material response parameters. Calculations are shown for examples that include the valence-core coherences for a vibrational monomer and for Frenkel and charge transfer electronic exciton states, which in the x-ray absorption near-edge structure spectral region has the potential to resolve the population and coherence contributions in the atomic localized basis.

Effective hydrodynamic modeling is crucial for accurately predicting fluid-particle interactions in diverse fields such as biophysics and materials science. Developing and implementing hydrodynamic algorithms is challenging due to the complexity of fluid dynamics, necessitating efficient management of large-scale computations and sophisticated boundary conditions. Furthermore, adapting these algorithms for use on massively parallel architectures such as GPUs adds an additional layer of complexity. This paper presents the libMobility software library, which offers a suite of CUDA-enabled solvers for simulating hydrodynamic interactions in particulate systems at the Rotne-Prager-Yamakawa level. The library facilitates precise simulations of particle displacements influenced by external forces and torques, including both the deterministic and stochastic components. Notable features of libMobility include its ability to handle linear and angular displacements, thermal fluctuations, and various domain geometries effectively. With an interface in Python, libMobility provides comprehensive tools for researchers in computational fluid dynamics and related fields to simulate particle mobility efficiently. This article details the technical architecture, functionality, and wide-ranging applications of libMobility. libMobility is available at https://github.com/stochasticHydroTools/libMobility.