A non-empirical minimal atomic multipole expansion (MAME) defines atomic charges or higher multipoles that reproduce electrostatic potential outside molecules. MAME eliminates problems associated with redundancy and with statistical sampling, and produces atomic multipoles in line with chemical intuition.
Buckingham expansion is important for understanding molecular multipoles and (hyper)polarizabilities. In this study, we give a complete derivation of Buckingham expansion in the traced form using successive Taylor series. Based on such derivation, a general Buckingham expansion in the traced form is proposed, and from which numerical calculations with finite field method of high accuracy can be achieved. The transformations from the traced multipoles and multipole-multipole polarizabilities to the corresponding traceless counterparts are realized with an auxiliary traced electric field gradien…
The accurate description of electrostatic interactions remains a challenging problem for fitted potential-energy functions. The commonly used fixed partial-charge approximation fails to reproduce the electrostatic potential at short range due to its insensitivity to conformational changes and anisotropic effects. At the same time, possibly more accurate machine-learned (ML) potentials struggle with the long-range behaviour due to their inherent locality ansatz. Employing a multipole expansion offers in principle an exact treatment of the electrostatic potential such that the long-range and sho…
GMP-Featurizer is a lightweight, accurate, efficient, and scalable software package for calculating the Gaussian Multipole (GMP) features \cite{GMP} for a variety of atomic systems with elements across the periodic table. Starting from the GMP feature computation module from AmpTorch \cite{amptorch}, the capability of GMP-Featurizer has since been greatly improved, including its accuracy and efficiency, as well as the ability to parallelize on different cores, even machines. Moreover, this python package only has very few dependencies that are all standard python libraries, plus cffi for C++ c…
Polarizable atomic multipoles for learning long-range electrostatics
Department of Chemistry, UC Berkeley, California 94720, United States（加州大学伯克利分校化学系）；Bakar Institute of Digital Materials for the Planet, UC Berkeley, California 94720, United States（为地球的数字材料巴卡研究所，加州大学伯克利分校）；Lawrence Livermore National Laboratory, Livermore, CA, USA（劳伦斯利弗莫尔国家实验室）；Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States（劳伦斯伯克利国家实验室化学科学部）
Atom-centered electric multipole moments dynamically generated from QM/MM MD simulations
Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院计算化学与生物化学实验室）；DTU Chemistry, Technical University of Denmark（丹麦技术大学化学系）
The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric response still solves the electrostatic problem inefficiently or not at all for solutes larger than $\approx 10$ non-hydrogen atoms. In existing MPE parameterizations, the resulting systematic underestimation of the electrostatic solute-solvent interaction is presently compensated for by a systematic overestimation of non-electrostatic attractive interactions. Ev…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of electrostatic interaction under periodic boundary condition. A standard remedy for the problem is to consider a hypothetical homogeneous background charge density to neutralize the total system. Here, we present a new expression for the evaluation of electrostatic interactions for the system including the background charge by fast multipole method (FMM). Further, an ef…
The structure and stability of atomic and molecular systems with van der Waals (vdW) bonding are often determined by the interplay between attractive dispersion interactions and repulsive interactions caused by electron confinement. Arising due to different mechanisms -- electron correlation for dispersion and the Pauli exclusion principle for exchange-repulsion -- these interactions do not appear to have a straightforward connection. In this paper, we use a coarse-grained approach for evaluating the exchange energy for two coupled quantum Drude oscillators and investigate the mutual compensat…
Charge regulation is an important aspect of electrostatics in biological and colloidal systems, where the charges are generally not fixed, but depend on the environmental variables. Here, we analyze the charge regulation mechanism in patchy, inhomogeneously charged spherical particles, such as globular proteins, colloids, or viruses. Together with the multipole expansion of inhomogeneously charged spherical surfaces, the charge regulation mechanism on the level of linear approximation is shown to lead to a mixing between different multipole moments depending on their capacitance -- the respons…
We study the formation of C$_{18}$H and C$_{18}$H$_2$ by irradiating a cyclo[$18$]carbon molecule with atomic and molecular hydrogen at impact energy, $E$, in the range of 0.5-25 eV. We utilize the density-functional tight-binding method to perform molecular dynamics simulations to emulate the interaction of a carbon ring when colliding with atomic or molecular hydrogen. From our results, the formation of the C$_{18}$H molecules is likely to occur upon irradiating by H atoms at $E < 10$ eV and by H$_2$ molecules at $2 < E < 15$ eV center of mass energy. Formation of C$_{18}$H$_2$ molecules is …
Leveraging ab initio data at scale has enabled the development of machine learning models capable of extremely accurate and fast molecular property prediction. A central paradigm of many previous works focuses on generating predictions for only a fixed set of properties. Recent lines of research instead aim to explicitly learn the electronic structure via molecular wavefunctions from which other quantum chemical properties can directly be derived. While previous methods generate predictions as a function of only the atomic configuration, in this work we present an alternate approach that direc…
'Oriented external electric fields (OEEFs)' have been shown to have great potential in being able to provide unprecedented control of chemical reactions, catalysis and selectivity with applications ranging from H2 storage to molecular machines. We report a theoretical study of the atomic origins of molecular changes due to OEEFs; understanding the characteristics of OEEF-induced couplings between atomic and molecular properties is an important step toward comprehensive understanding of the effects of strong external fields on molecular structure, stability, and reactivity. We focus on the atom…
This editorial introduces the J. Phys. B: Atomic, Molecular and Optical Physics Special Issue "Atomic and Molecular Processes in the Ultracold Regime, the Chemical Regime and Astrophysics" dedicated to Professor Alexander Dalgarno (1928-2015). After a brief biographical review, short summaries of the contributed papers and their relations to some of Prof. Dalgarno's work are given.
We show that the pressure acting on atoms and molecular systems within the compression cavity of the eXtreme-Pressure Polarizable Continuum method can be expressed in terms of the electron density of the systems and of the Pauli-repulsion confining potential. The analytical expression holds for spherical cavities as well as for cavities constructed from van der Waals spheres of the constituting atoms of the molecular systems.
We develop a new scheme for determining molecular partial atomic charges (PACs) with external electrostatic potential (ESP) closely mimicking that of the molecule. The PACs are the "minimal corrections" to a reference-set of PACs necessary for reproducing exactly the tensor components of the Cartesian zero- first- and second- molecular electrostatic multipoles. We evaluate the quality of ESP reproduction when "minimally correcting" (MC) Mulliken, Hirshfeld or iterated-Hirshfeld reference PACs. In all these cases the MC-PACs significantly improve the ESP while preserving the reference PACs' inv…
Atomic effective one-electron potentials in a compact analytic form in terms of a few Gaussian charge distributions are developed, for Hydrogen through Nobelium, for starting molecular electronic structure calculations by a simple diagonalization. For each element, all terms but one are optimized in an isolated-atom Hartree--Fock calculation, and the last one is parametrized on a set of molecules. This one-parameter-per-atom model gives a good starting guess for typical molecules and may be of interest even on its own.
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: 1) atomic and molecular absorption spectra, 2) atomic and molecular emission spectra, 3) transition linestrengths, and 4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermody…
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that …
Not long after metastable xenon was photoionized in a magneto-optical trap, groups in Europe and North America found that similar states of ionized gas evolved spontaneously from state-selected, high principal quantum number Rydberg gases. Studies of atomic xenon and molecular nitric oxide entrained in a supersonically cooled molecular beam subsequently showed much the same final state evolved from a sequence of prompt Penning ionization and electron-impact avalanche to plasma, well-described by coupled rate-equation simulations. But, measured over longer times, the molecular ultracold plasma …
