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Using the energy components associated with density-functional theory (DFT) calculations and various descriptors from the density-functional reactivity theory (conceptual DFT), we explore which chemical effects are most important for determining the ordering the conformers of the twenty natural amino acids in terms of their relative energetic stability. Electrostatic and steric (alternatively, electrostatic and exchange–correlation) interactions are found to be most descriptive of conformer stability. We also introduce an approach for determining how well one or more descriptors order the conformers, without requiring a linear (or any other) correlation between the descriptors. This ordering/ranking paradigm is likely to be useful in many other contexts also. [ABSTRACT FROM AUTHOR]

One can partition the molecular density into its atomic contributions by minimizing the divergence of the atom-in-molecule densities from their corresponding reference pro-atomic densities, subject to the constraint that the sum of the atom-in-molecule densities is the total molecular density. We expose conditions on the divergence measure that are necessary, and sufficient, to recover the popular Hirshfeld partitioning. Specifically, among all local measures of the divergence between two probability distribution functions, the Hirshfeld partitioning is obtained only for f-divergences. [ABSTRACT FROM AUTHOR]

The atoms in molecules associated with the Hirshfeld partitioning minimize the generalized Hellinger-Bhattacharya distance to the reference pro-atom densities. Moreover, the reference proatoms can be chosen by minimizing the distance between the pro-molecule density and the true molecular density. This provides an alternative to both the heuristic "stockholder" and the mathematical information-theoretic interpretations of the Hirshfeld partitioning. These results extend to any member of the family of f-divergences. [ABSTRACT FROM AUTHOR]

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope. [ABSTRACT FROM AUTHOR]

We argue that when one divides a molecular property into atom‐in‐a‐molecule contributions, one should perform the division based on the property density of the quantity being partitioned. This is opposition to the normal approach, where the electron density is given a privileged role in defining the properties of atoms‐in‐a‐molecule. Because partitioning each molecular property based on its own property density is inconvenient, we design a reference‐free approach that does not (directly) refer atomic property densities. Specifically, we propose a stockholder partitioning method based on relative influence of a molecule's atomic nuclei on the electrons at a given point in space. The resulting method does not depend on an “arbitrary” choice of reference atoms and it has some favorable properties, including the fact that all of the electron density at an atomic nucleus is assigned to that nucleus and the fact all the atoms in a molecule decay at a uniform asymptotic rate. Unfortunately, the resulting model is not easily applied to spatially degenerate ground states. Furthermore, the practical realizations of this strategy that we tried here gave disappointing numerical results. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way that clarifies the enormous freedom one has within the information-theoretic ansatz. [ABSTRACT FROM AUTHOR]

Atoms in molecules methods that rely on reference promolecular densities typically require that one define, or otherwise determine, the densities of unbound atomic anions. Whereas the isolated atomic polyanions are always physically and computationally unbound, monoanions can be either physically bound but computationally unbound (like the oxygen anion at the Hartree-Fock level of theory), or physically unbound but computationally bound (like the nitrogen anion using many DFT methods with a basis set including diffuse functions). Depending on the level of theory and basis set used, the densities of negatively charged atomic ions can decay very slowly and even be nonmonotonically decreasing. These delocalized anionic densities induce ill-behaved atomic properties for compounds containing highly reduced atoms. To treat the problem of unphysical proatom densities in iterative Hirshfeld methods, we compute the smallest (typically fractional) nuclear charge to bind all electrons, called the effective nuclear charge $$ {Z}_{\mathrm{A}}^{\mathrm{eff}} $$ of an atom A. When $$ {Z}_{\mathrm{A}}^{\mathrm{eff}}>{Z}_{\mathrm{A}} $$ at a given level of theory, the scaled density corresponding to the effective nuclear charge is used as the negatively charged proatom density. This novel approach dramatically improves the computational robustness of the iterative Hirshfeld partitioning scheme. [ABSTRACT FROM AUTHOR]

We establish the physical origins of chemical transferability from the perspective of the nearsightedness of electronic matter. To do this, we explicitly evaluate the response of electron density to a change in the system, at constant chemical potential, by computing the softness kernel, s(r, r'). The softness kernel is nearsighted, indicating that under constant-chemical-potential conditions like dilute solutions changing the composition of the molecule at r has only local effects and does not have any significant impact on the reactivity at positions r' far away from point r. This locality principle elucidates the transferability of functional groups in chemistry. [ABSTRACT FROM AUTHOR]

We define the densities of atoms in molecules so that their Bregman divergence from reference proatom densities is minimized. This generalizes the information-theoretic approach to atoms in molecules and under reasonable assumptions, results in a formulation that resembles the Hirshfeld partitioning. In general, Bregman partitionings are intrinsically nonlocal, and this means that this formulation, while mathematically elegant, is computationally unwieldy. [ABSTRACT FROM AUTHOR]

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade. [ABSTRACT FROM AUTHOR]

We show that the statistical divergence measures associated with non-extensive thermodynamic entropy functions-specifically the Tsallis, Réyni, Sharma-Mittal, supraextensive, and H-divergences-are associated with the Hirshfeld atoms-in-molecules partitioning. This extends the treatment of Nalewajski and Parr (J Phys Chem A 109:3957-3959, 2005), (for the extensive Shannon entropy) to non-extensive entropy measures. It also extends the work of Heidar-Zadeh and Ayers (J Chem Phys 142(4):044107, 2015), (for divergence measures that are local density functionals) to non-local functionals. These results dramatically extend the mathematical framework that one can use for similarity-based atoms-in-molecules partitioning. [ABSTRACT FROM AUTHOR]

We consider the problem of defining an appropriate local descriptor corresponding to an arbitrary global descriptor. Although it does not seem easy to rigorously and uniquely define local analogues of derived global descriptors (e.g., the electrophilicity) or the fundamental global descriptors associated with the canonical ensemble (e.g., the hardness), the local response of these global descriptors can be defined unambiguously. We look at the local response of the global electrophilicity and compare it to the conventional, ad hoc, definition of the local electrophilicity. The local response of global nucleofugality and electrofugality is also discussed. [ABSTRACT FROM AUTHOR]

We present explicit formulas for arbitrary-order derivatives of the energy, grand potential, electron density, and higher-order response functions with respect to the number of electrons, and the chemical potential for any smooth and differentiable model of the energy versus the number of electrons. The resulting expressions for global reactivity descriptors (hyperhardnesses and hypersoftnesses), local reactivity descriptors (hyperFukui functions and local hypersoftnesses), and nonlocal response functions are easy to evaluate computationally. Specifically, the explicit formulas for global/local/nonlocal hypersoftnesses of arbitrary order are derived using Bell polynomials. Explicit expressions for global and local hypersoftness indicators up to fifth order are presented. [ABSTRACT FROM AUTHOR]

This contribution deals with the subsystem variational procedure within the context of the quantum theory of atoms in positronic molecules (QTAIPM). Before introducing the subsystem energy functional termed as joint subsystem energy functional, a novel notation and the combination strategy are disclosed in detail by restating the positronic subsystem hypervirial theorem. They are employed in proposing the proper subsystem energy functional, the validity of which is checked by various criteria. The zero flux surfaces of the joint density distribution are used to define the topological atoms in the positronic molecules, and they are incorporated into the subsystem variational procedure as proper real space boundary conditions. The variational procedure finally yields the flux of the joint current property density that also appears in the positronic subsystem hypervirial theorem. At every stage, the corresponding equations for the purely electronic systems within the context of the quantum theory of atoms in molecules (QTAIM) are presented to clearly reveal the analogy between these two formalisms and to emphasize the importance of combining the property density distributions in the QTAIPM. The presented material demonstrates the internal consistency of the whole framework and discloses the fact that the QTAIM must be regarded as a variant of the QTAIPM. Furthermore, this formalism promises an extended QTAIM, which is hoped to resolve the issue of molecular structure beyond the clamp nuclei approximation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 [ABSTRACT FROM AUTHOR]

We provide a general (yet elementary) proof of Pearson's hard/soft acid/base principle. Contrary to previous attempts to justify this rule, we go beyond the venerable parabolic model of Parr and Pearson. This new treatment encompasses more realistic E versus N dependencies, while emphasizing the importance of the correct normalization of these models. [ABSTRACT FROM AUTHOR]

We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties. [ABSTRACT FROM AUTHOR]

We discuss an extension of the venerable Parr‐Pearson parabolic charge transfer model that explicitly includes 3rd order effects. We then use this new model to provide new arguments supporting the validity of Parr and Yang's "|Δμ| big is good" (DMB) principle. Additionally, we show how to re‐derive this principle from the Parr‐Pearson parabolic model, using simpler arguments than those presented in our previous proof of the DMB rule. [ABSTRACT FROM AUTHOR]

We analyze the problem of selecting the model that best describes a given dataset. We focus on the case where the best model is the one with the smallest error, respect to the reference data. To select the best model, we consider two components: (a) an error measure to compare individual data points, and (b) a function that combines the individual errors for all the points. We show that working with the most general definition of consistency, it is impossible to extend individual error measures in a way that provides a unanimous consensus about which is the best model. We also prove that, in the best case, modifying the notion of consistency leads to expressions that are too ill-behaved to be of any practical utility. These results show that selecting the model that best describes a dataset depends heavily on the way one measures the individual errors, even if these measures are consistent. [ABSTRACT FROM AUTHOR]

The numerical ill‐conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater‐type functions is overcome by using the (extended) Kullback–Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non‐negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non‐negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non‐negative basis functions. We present a fixed‐point iteration method for optimizing the Kullback–Leibler divergence and compare it to conventional gradient‐based optimization methods. These algorithms are released through the free and open‐source BFit package, which also includes a L2‐norm squared optimization routine applicable to any square‐integrable scalar function. [ABSTRACT FROM AUTHOR]

Fanpy is a free and open‐source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N‐electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin‐orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library. [ABSTRACT FROM AUTHOR]

Using results from atomic spectroscopy, we show that there are two types of flat-planes conditions. The first type of flat-planes condition occurs when the energy as a function of the number of electrons of each spin, Nα and Nβ, has a derivative discontinuity on a line segment where the number of electrons, Nα + Nβ, is an integer. The second type of flat-planes condition occurs when the energy has a derivative discontinuity on a line segment where the spin polarization, Nα - Nβ, is an integer, but does not have a discontinuity associated with an integer number of electrons. Type 2 flat planes are rare-we observed just 15 type 2 flat-planes conditions out of the 4884 cases we tested-but their mere existence has implications for the design of exchange-correlation energy density functionals. To facilitate the development of functionals that have the correct behavior with respect to both fractional number of electrons and fractional spin polarization, we present a dataset for the chromium atom and its ions that can be used to test new functionals. [ABSTRACT FROM AUTHOR]

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library. [ABSTRACT FROM AUTHOR]

The paper collects the answers of the authors to the following questions:Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes?Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts?How can one use the results of a partition scheme to improve the clarity of definitions of concepts?Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process?To what extent does/can/should investigated systems influence the choice of a particular partition scheme?Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general?Is there any interest in developing common benchmarks and test sets for cross‐validation of methods?Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle?In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]