Journal of Chemical Physics最新文献

Integrals for Gaussian-type orbitals are the basis of every quantum chemical calculation. In this work, we present the efficient implementation of nuclear attraction and of two- and three-center electron repulsion integral calculations based on the Rys quadratures. It was found that some types of electron repulsion integrals can be calculated using modified Rys quadratures with fewer roots. Despite the overall effect of this modification being shown to be small, a 1.6-fold speed-up of some types of integral calculations was achieved. Overall, nuclear attraction integral calculations were shown to be 8-10 times faster compared to LIBINT in electrostatic potential calculation tasks. The speed of three-center electron repulsion integrals calculation was enhanced by a factor of 2-4 compared to LIBINT.

We develop a semi-analytic theory for describing nonadiabatic bound-bound, free-bound, bound-free, and free-free photoprocesses in heteronuclear ions in the regime of the superlinear potential energy curve crossing. It extends the previous semiclassical method for calculating the absorption and emission spectra of strongly and moderately bound diatomic species based on the linear curve crossing model and can be used for molecules and ions with small dissociation energies, D0 ≲ kBT. The use of quasicontinuum approximation for rovibrational levels allows us to give a unified description of the integral contributions of the discrete and continuous spectra of the molecular species with linear and superlinear crossings to the effective cross sections and rate coefficients of the radiative processes in the systems studied. Specific calculations were performed for the excimer-like NeXe+ ion (DeNeXe+=37.3 meV). Potential energy curves and dipole transition matrix elements are evaluated using ab initio multi-reference calculations with a perturbative description of relativistic effects. In contrast to ArXe+ and KrXe+ ions studied previously, the main contributions to the absorption spectra of NeXe+ are due to bound-bound transitions and photoassociation. The emission spectra at room temperatures are determined predominantly by the bound-bound transitions, while at temperatures above 450 K, the most significant contribution to the radiation is made by bound-free phototransitions. Our calculations are in good agreement with the available experimental data. The results obtained are of interest for chemical physics, spectroscopy of weakly bound molecular systems, and physics of radiative processes in gases and plasmas, as well as for the kinetics of active media of excilamps and gas lasers based on noble gas mixtures.

We present the first study of the rotational excitation of AlCl(X1Σ+) induced by collisions with H2. We have calculated a four dimensional potential energy surface (PES) to describe the AlCl-H2 interaction, with AlCl and H2 being treated as rigid rotors. This PES has been computed using the explicitly correlated coupled-cluster method with single, double, and perturbative triple excitation in conjunction with the augmented-correlation consistent-polarized valence triple zeta basis set. Then, we have calculated the rotational excitation cross sections between the first 41 rotational levels of AlCl induced by H2 collisions using the time-independent quantum mechanical close-coupling and coupled-states formalisms. Convergence tests revealed that the inclusion of excited para-H2 energy levels in the rotational basis has a minor effect on the magnitude of the excitation cross sections. We also found that AlCl excitation cross sections induced by ortho-H2 collisions are in good agreement with those induced by para-H2 collisions. Hence, we limited the calculations to the excitation cross sections induced by H2 in its ground rotational state. To derive excitation rate coefficients for temperatures up to 250 K, the cross sections computed for energies up to 1500 cm-1 were averaged over a Maxwell-Boltzmann velocity distribution. The new rate coefficients were compared to those available for the AlCl-He collisional system, and major differences were found at high temperature, showing that actual AlCl-H2 rate coefficients should be used for accurate astrophysical models. The new data are expected to play a crucial role in the modeling of AlCl observational spectra and will help in better constraining its abundance in space.

We present an efficient algorithm for constructing an all-electron periodic Coulomb matrix based on Ewald summation combined with the Fourier-transformed Coulomb method. The short-range contributions involving compact densities are evaluated in real space using standard Gaussian density fitting. For the long-range contributions, we introduce an integral-direct plane wave density fitting scheme that is applicable to both compact and diffuse densities. The resulting method achieves orders-of-magnitude speedups for prototypical solid-state systems compared to a closely related approach, the range-separated density fitting method. Using the dispersion-corrected PBE functional with all-electron Dunning and Karlsruhe basis sets, we apply our method to compute the cohesive energy of the benzene crystal and the adsorption energy of CO on the MgO(001) surface. These results are in good agreement with existing literature. Our approach enables efficient Gaussian-based semi-local density functional calculations using dense k-point meshes and traditional molecular Gaussian basis sets.

We study the translocation of a flexible polymer through extended patterned pores using molecular dynamics (MD) simulations. We consider cylindrical and conical pore geometries that can be controlled by the angle of the pore apex α. We obtained the average translocation time ⟨τ⟩ for various chain lengths N and the length of the pores Lp for various values α and found that ⟨τ⟩ scales as ⟨τ⟩∼NγFLpNϕ, with exponents γ = 3.00 ± 0.05 and ϕ = 1.50 ± 0.05 for both patterned and unpatterned pores, respectively.

Polyethyleneimine (PEI)-functionalized nanochannels have been extensively exploited in ion gating and biosensing. It is of great significance to explore their conductance determining ion-surface interaction and ionic transport at the nanoscale. Here, pH-regulated conductance of PEI-coated nanochannels is theoretically studied. The results suggest that coating PEI may improve nanochannel conductance in different ways depending on the surface charge of nanochannels. The conductance of a PEI-coated PET nanochannel whose surface charge is assumed to be constant for simplicity is weakly changed and then decreased to that of a non-PEI-coated PET nanochannel with increasing pH, which is consistent with the reported experimental results. The conductance of a PEI-coated silica nanochannel, whose surface charge largely depends on pH, ion concentration, and nanochannel radius, is significantly increased and, subsequently, decreased to that of a non-PEI-coated silica nanochannel as pH rises, which is rarely reported in experiments. This work provides a fundamental framework to investigate the conductance of PEI-coated nanochannels, and the PEI-coated silica nanochannels with unique pH-dependent conductance may be explored in the construction of mesoporous silica thin films for biomedical analytical applications.

Time-resolved third-order and fifth-order CARS experiments were employed to systematically investigate the vibrational dynamics of liquid nitromethane (NM) molecules in both fundamental and overtone bands, and the overtone vibrational dephasing parameters of NM were reported for the first time. The experimental findings reveal that overtone vibrations exhibit a notably faster dephasing process than corresponding fundamental vibrations. This phenomenon arises from the higher energy levels of overtone vibrations, which render them more susceptible to strong intermolecular interactions within the condensed-phase environment. Among the main vibrational modes of NM, the dephasing lifetime of the C-N stretching vibration is remarkably longer than that of other modes, and even the overtone lifetime is longer than the fundamental lifetime of other modes. It is indicated that when NM is excited by external stimuli, energy has a high probability of depositing on the C-N bond, which in turn brings this bond to a high vibrational level. This inference helps account for the observation that C-N bond cleavage acts as the primary initial reaction channel in the pyrolysis and photolysis of NM. Molecular vibrations, especially the vibrations in high vibrational excited states, are closely associated with the chemical reactions of molecules. This study contributes to a better understanding of the vibrational energy localization mechanism and the subsequent molecular dissociation in condensed-phase energetic materials.

Combining classical density functional theory (cDFT) with quantum mechanics (QM) methods offers a computationally efficient alternative to traditional QM/molecular mechanics (MM) approaches for modeling mixed quantum-classical systems at finite temperatures. However, both QM/MM and QM/cDFT rely on somewhat ambiguous approximations, the two major ones being: (i) the definition of the QM and MM regions as well as the description of their coupling, and (ii) the choice of the methods and levels of approximation made to describe each region. This paper addresses the second point and develops an exact theoretical framework that allows us to clarify the approximations involved in the QM/cDFT formulation. We, therefore, establish a comprehensive density functional theory (DFT) framework for mixed quantum-classical systems within the canonical ensemble. We start by recalling the expression of the adiabatic equilibrium density matrix for a mixed system made of Nqm quantum and Nmm classical particles, which can be related to a partial Wigner transform. Then, we propose a variational formulation of the Helmholtz free energy in terms of the full, non-equilibrium, QM/MM density matrix. Taking advantage of permutational symmetry and thanks to constrained-search methods, we reformulate the computation of the Helmholtz free energy using only the quantum and classical one-body densities. Therefore, this paper generalizes both cDFT and electronic DFT (eDFT) to QM/MM systems. We then reformulate the functional to make the standard eDFT and cDFT Levy-Lieb functionals explicitly appear, together with a new universal correlation functional for QM/MM systems. A mean-field approximation is finally introduced in the context of solvation problems, and we discuss its connection with several existing mixed cDFT-eDFT schemes. An extension to the semi-grand canonical ensemble, where the number of classical particles is allowed to fluctuate, is provided in the supplementary material.

An accurate description of electronic polarization is fundamental to modeling protein interactions and dynamics. Despite its importance, polarization is frequently omitted in classical force fields, while existing polarizable models are hindered by parameterization complexity, high computational cost, or limited resolution. We present a novel, efficient method for calculating protein polarization energies. Our method computes local electric fields at atomic sites, decomposes them into bond-parallel and perpendicular components, and uses environment-specific, anisotropic atomic polarizabilities fitted to accurate quantum-chemical calculations. The model accurately reproduces quantum-mechanical polarization energies for amino-acid monomers, dimers, trimers, and small proteins. Its computational efficiency enables application to large, explicitly solvated proteins, achieving excellent agreement with benchmark data at a minimal computational cost. We demonstrate its scalability by applying it to large, solvated proteins, providing a practical path for incorporating polarization into biomolecular simulations.

This study presents the implementation of the linear response function for 1D periodic systems at the coupled cluster with single and double excitations with periodic boundary conditions level (LR-CCSD-PBC) for the calculation of the frequency-dependent electric dipole-electric dipole polarizability tensor, α(ω), using the modified velocity gauge (MVG) formalism. We compare this approach with the length gauge (LG) formalism that we presented in a previous study [Caricato et al., APL Comput. Phys. 1, 026107 (2025)] in terms of theoretical analysis and computational results. The calculations on molecular systems with large Dunning basis sets, including diffuse functions, show a smooth convergence toward the complete basis set limit (CBS) with both formalisms, but LG and MVG converge to different values when CCSD provides an incomplete treatment of electron correlation. With the small basis sets used in the PBC calculations, the difference between the gauge formalisms increases due to basis set incompleteness. For the PBC calculations on 1D periodic systems, the MVG formalism shows a faster convergence toward the thermodynamic limit with k sampling compared to LG. Furthermore, the MVG formalism provides perfect agreement between PBC and long molecular cluster models. This is not the case for LG due to the so-called missing integer issue. However, a comparison with the molecular data suggests that the LG-PBC results with the small basis set affordable in this study are closer to the CBS results than those with MVG. This study represents a further step forward in the simulation of optical response properties for solid-state materials with systematically improvable quantum mechanical methods.