Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $σ$-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the $σ$-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the Restricted Electrostatic Potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The $σ$-hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.
Polyhalogenated compounds are common in industrial, agricultural, and environmental applications. These compounds contain more halogen bonds than monohalogenated compounds. The presence of coupled σ-holes in the covalent halogen atoms, which demonstrates strong interplay in halogen bonds, should be carefully evaluated in force field optimization. In this study, a polarizable ellipsoidal force field model was successfully applied to many possible halogenated benzenes. The symmetry of the fitted parameters was reproduced without any additional restrictions. The optimized parameters for the aniso…
This study is focused on the effects of cosmic rays (solar activity) and halogenated molecules (mainly chlorofluorocarbons-CFCs) on atmospheric O3 depletion and global climate change. Brief reviews are first given on the cosmic-ray-driven electron-induced-reaction (CRE) theory for O3 depletion and the warming theory of CFCs for climate change. Then natural and anthropogenic contributions are examined in detail and separated well through in-depth statistical analyses of comprehensive measured datasets. For O3 loss, new statistical analyses of the CRE equation with observed data of total O3 and …
To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP, called $σ$-hole, is a concept of central importance for halogen bonding. We aim at simplifying the view on $σ$-holes and provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as of biomolecular complexes and attempt to improve the intuition of chemists when dealing with h…
We propose using halogenated organic dyes as nanoprobes for electric field and show their greatly enhanced Stark coefficients using density functional theory (DFT) calculations. We analyse halogenated variants of three molecules that have been of interest for cryogenic single molecule spectroscopy, perylene, terrylene, and dibenzoterrylene, with the zero-phonon optical transitions at blue, red, and near infrared. Out of all the combinations of halides and binding sites that are calculated, we have found that fluorination of the optimum binding site induces a dipole difference between ground an…
We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling of computational cost in system size is demonstrated for saturated polymers with up to sub-mesoscale lengths.
The interaction within a hybrid system consisting of a spherical metal nanoparticle and a nearby organic dye molecule is formulated in a combined quantum-classical approach. Whereas the nanoparticle's polarization field is treated in classical multipole form, the electronic charge density of the molecule is described quantum mechanically. An efficient solution of the resulting self-consistency problem becomes possible by using the discrete representation of the charge density in terms of atom-centered Mulliken charges within the density functional theory-based tight binding (DFTB) approach. Re…
A linear-scaling algorithm is presented for computing the Hartree-Fock (HF) exchange matrix using concentric atomic density fitting. The algorithm utilizes the stronger distance dependence of the three-center electron repulsion integrals along with the rapid decay of the density matrix to accelerate the construction of the exchange matrix. The new algorithm is tested with computations on systems with up to 1536 atoms and 15585 basis functions, the latter of which represents, to our knowledge, the largest quadruple-zeta HF computation ever performed. Our method handles screening of high angular…
We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis-set representation (Fabian et al. WIREs Comput Mol Sci. 2019;e1412. https://doi.org/10.1002/wcms.1412) and apply it to Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the…
Generalized gradient approximated (GGA) density functional theory (DFT) typically overestimates polarizability and bond-lengths, and underestimates force constants of covalent bonds. To overcome this problem we show that one can use empirical force correcting atom centered potentials (FCACPs), parameterized for every nuclear species. Parameters are obtained through minimization of a penalty functional that explicitly encodes hybrid DFT forces and static polarizabilities of reference molecules. For hydrogen, fluorine, chlorine, and carbon the respective reference molecules consist of H$_2$, F$_…
Extracting a nitrile-centered, ether-assisted motif hierarchy for lithium-battery electrolyte design from billion-scale molecular space
University of Science and Technology of China（中国科学技术大学）；Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）；Suzhou Big Data & AI Research and Engineering Center（苏州大数据与人工智能研究与工程中心）；Contemporary Amperex Technology Co. Limited（宁德时代新能源科技股份有限公司）；AI for Science Institute（人工智能科学研究所）
Electronic structure calculation of atoms and molecules, in the past few decades has largely been dominated by density functional methods. This is primarily due to the fact that this can account for electron correlation effects in a rigorous, tractable manner keeping the computational cost at a manageable level. With recent advances in methodological development, algorithmic progress as well as computer technology, larger physical, chemical and biological systems are amenable to quantum mechanical calculations than ever before. Here we report the development of a new method for accurate reliab…
The electron density of a molecule or material has recently received major attention as a target quantity of machine-learning models. A natural choice to construct a model that yields transferable and linear-scaling predictions is to represent the scalar field using a multi-centered atomic basis analogous to that routinely used in density fitting approximations. However, the non-orthogonality of the basis poses challenges for the learning exercise, as it requires accounting for all the atomic density components at once. We devise a gradient-based approach to directly minimize the loss function…
Density functional theory (DFT) has emerged as one of the most versatile and lucrative approaches in electronic structure calculations of many-electron systems in past four decades. Here we give an account of the development of a variational DFT method for atoms and molecules \emph{completely} in a Cartesian grid. The non-relativistic Kohn-Sham equation is solved by using an LCAO-MO ansatz. Atom-centered localized basis set, electron density, molecular orbitals, two-body potentials are directly constructed on the grid. We adopt a Fourier convolution method for classical Coulomb potentials by m…
This chapter concerns with the recent development of a new DFT methodology for accurate, reliable prediction of many-electron systems. Background, need for such a scheme, major difficulties encountered, as well as their potential remedies are discussed at some length. Within the realm of non relativistic Hohenberg-Kohn-Sham (HKS) DFT and making use of the familiar LCAO-MO principle, relevant KS eigenvalue problem is solved numerically. Unlike the commonly used atom-centered grid (ACG), here we employ a 3D cartesian coordinate grid (CCG) to build atom-centered localized basis set, electron dens…
We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies via machine learning. The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the undesirable scaling of the latter with increasing number of different elements in a chemical system. The performance of these two descriptors is compared using them as inputs in high-dimensional neural network potentials (HDNNPs), employing the molecular structures and associated e…
A common way to evaluate electronic integrals for polyatomic molecules is to use Becke's partitioning scheme [J. Chem. Phys.88, 2547 (1988)] in conjunction with overlapping grids centered at each atomic site. The Becke scheme was designed for integrands that fall off rapidly at large distances, such as those approximating bound electronic states. When applied to states in the electronic continuum, however, Becke scheme exhibits slow convergence and it is highly redundant. Here, we present a modified version of Becke scheme that is applicable to functions of the electronic continuum, such as th…
Static electric response properties of atoms and molecules are reported within the real-space Cartesian grid implementation of pseudopotential Kohn-Sham (KS) density functional theory (DFT). A detailed systematic investigation is made for a representative set of atoms and molecules, through a number of properties like total ground-state electronic energies, permanent dipole moment ($\bmμ$), static average dipole polarizability ($\overlineα$). This is further extended to first-hyperpolarizability ($\bmβ$) in molecules. It employs a recently developed non-uniform grid-optimization technique, wit…
Liquid hydrocarbons are often modeled with fixed, symmetric, atom-centered charge distributions and Lennard-Jones interaction potentials that reproduce many properties of the bulk liquid. While useful for a wide variety of applications, such models cannot capture dielectric effects important in solvation, self-assembly, and reactivity. The dielectric constants of hydrocarbons, such as methane and ethane, physically arise from electronic polarization fluctuations induced by the fluctuating liquid environment. In this work, we present non-polarizable, fixed-charge models of methane and ethane th…
Symmetry considerations are at the core of the major frameworks used to provide an effective mathematical representation of atomic configurations that is then used in machine-learning models to predict the properties associated with each structure. In most cases, the models rely on a description of atom-centered environments, and are suitable to learn atomic properties, or global observables that can be decomposed into atomic contributions. Many quantities that are relevant for quantum mechanical calculations, however -- most notably the single-particle Hamiltonian matrix when written in an at…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, partic…
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose paramet…
Entangled two-photon absorption (ETPA) has recently become a topic of lively debate, mainly due to the apparent inconsistencies in the experimentally-reported ETPA cross sections of organic molecules. In this work, we provide a thorough experimental study of ETPA in the organic molecules Rhodamine B (RhB) and Zinc Tetraphenylporphirin (ZnTPP). The goal of this contribution is twofold: on one hand, it seeks to reproduce the results of previous experimental reports and, on the other, it aims to determine the effects of different temporal correlations -- introduced as a controllable time-delay be…
