APOST-3D: Chemical concepts from wavefunction analysis.

Open-source APOST-3D software features a large number of wavefunction analysis tools developed over the past 20 years, aiming at connecting classical chemical concepts with the electronic structure of molecules. APOST-3D relies on the identification of the atom in the molecule (AIM), and several analysis tools are implemented in the most general way so that they can be used in combination with any chosen AIM. Several Hilbert-space and real-space (fuzzy atom) AIM definitions are implemented.

Spurious Oscillations Caused by Density Functional Approximations: Who is to Blame? Exchange or Correlation?

We analyze the varying susceptibilities of different density functional approximations (DFAs) to present spurious oscillations on the profiles of several vibrational properties. Among other problems, these spurious oscillations cause significant errors in harmonic and anharmonic IR and Raman frequencies and intensities. This work hinges on a judicious strategy to dissect the exchange and correlation components of DFAs and pinpoint the origins of these oscillations.

All-Purpose Measure of Electron Correlation for Multireference Diagnostics.

We present an analytical relationship between two natural orbital occupancy-based indices, and , and two established electron correlation metrics: the leading term of a configuration interaction expansion, , and the diagnostic. Numerical validation revealed that and can effectively substitute for and , respectively. These indices offer three distinct advantages: (i) they are universally applicable across all electronic structure methods, (ii) their interpretation is more intuitive, and (iii) they can be readily incorporated into the development of hybrid electronic structure methods.

Reply to the Correspondence on "How Aromatic Are Molecular Nanorings? The Case of a Six-Porphyrin Nanoring".

A recent article by Anderson and co-workers challenges our conclusions on the aromaticity of the four oxidation states of a butadyine-linked six-porphyrin nanoring, based on the experimental H-NMR data and some recent calculations they have performed using the BLYP35 functional. Here, we show that BLYP35 should be taken with caution and demonstrate that the indirect evidence of a ring current from experimental H-NMR data is not a definite proof of aromaticity.

How Reliable Are Modern Density Functional Approximations to Simulate Vibrational Spectroscopies?

We show that properties of molecules with low-frequency modes calculated with density functional approximations (DFAs) suffer from spurious oscillations along the nuclear displacement coordinate due to numerical integration errors. Occasionally, the problem can be alleviated using extensive integration grids that compromise the favorable cost-accuracy ratio of DFAs. Since spurious oscillations are difficult to predict or identify, DFAs are exposed to severe performance errors in IR and Raman intensities and frequencies or vibrational contributions to any molecular property.

Natural range separation of the Coulomb hole.

A natural range separation of the Coulomb hole into two components, one of them being predominant at long interelectronic separations (h ) and the other at short distances (h ), is exhaustively analyzed throughout various examples that put forward the most relevant features of this approach and how they can be used to develop efficient ways to capture electron correlation. We show that h , which only depends on the first-order reduced density matrix, can be used to identify molecules with a predominant nondynamic correlation regime and differentiate between two types of nondynamic correlation, types A and B. Through the asymptotic properties of the hole components, we explain how h can retrieve the long-range part of electron correlation.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

How Aromatic Are Molecular Nanorings? The Case of a Six-Porphyrin Nanoring*.

Large conjugated rings with persistent currents are novel promising structures in molecular-scale electronics. A six-porphyrin nanoring structure that allegedly sustained an aromatic ring current involving 78π electrons was recently synthesized. We provide here compelling evidence that this molecule is not aromatic, contrary to what was inferred from the analysis of H-NMR data and computational calculations that suffer from large delocalization errors.

Role of Dispersion Interactions in Endohedral TM@(ZnS) Structures.

II-VI semiconducting materials are gaining attention due to their optoelectronic properties. Moreover, the addition of transition metals, TMs, might give them magnetic properties. The location and distance of the TM are crucial in determining such magnetic properties.

How Many Electrons Does a Molecular Electride Hold?

Electrides are very peculiar ionic compounds where electrons occupy the anionic positions. In a crystal lattice, these isolated electrons often form channels or surfaces, furnishing electrides with many traits with promising technological applications. Despite their huge potential, thus far, only a few stable electrides have been produced because of the intricate synthesis they entail.

How do the Hückel and Baird Rules Fade away in Annulenes?

Two of the most popular rules to characterize the aromaticity of molecules are those due to Hückel and Baird, which govern the aromaticity of singlet and triplet states. In this work, we study how these rules fade away as the ring structure increases and an optimal overlap between orbitals is no longer possible due to geometrical restrictions. To this end, we study the lowest-lying singlet and triplet states of neutral annulenes with an even number of carbon atoms between four and eighteen.

Singling Out Dynamic and Nondynamic Correlation.

The correlation part of the pair density is separated into two components, one of them being predominant at short electronic ranges and the other at long ranges. The analysis of the intracular part of these components permits to classify molecular systems according to the prevailing correlation: dynamic or nondynamic. The study of the long-range asymptotics reveals the key component of the pair density that is responsible for the description of London dispersion forces and a universal decay with the interelectronic distance.

Nine questions on energy decomposition analysis.

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.

The Coulomb Hole of the Ne Atom.

We analyze the Coulomb hole of Ne from highly-accurate CISD wave functions obtained from optimized even-tempered basis sets. Using a two-fold extrapolation procedure we obtain highly accurate results that recover 97 % of the correlation energy. We confirm the existence of a shoulder in the short-range region of the Coulomb hole of the Ne atom, which is due to an internal reorganization of the -shell caused by electron correlation of the core electrons.

Comprehensive benchmarking of density matrix functional approximations.

The energy usually serves as a yardstick in assessing the performance of approximate methods in computational chemistry. After all, these methods are mostly used for the calculation of the electronic energy of chemical systems. However, computational methods should be also aimed at reproducing other properties, such strategy leading to more robust approximations with a wider range of applicability.

Local Descriptors of Dynamic and Nondynamic Correlation.

Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important.

Electron correlation effects in third-order densities.

The electronic energy of a system of fermions can be obtained from the second-order reduced density matrix through the contracted Schrödinger equation or its anti-Hermitian counterpart. Both energy expressions depend on the third-order reduced density matrix (3-RDM) which is usually approximated from lower-order densities. The accuracy of these methods depends critically on the set of N-representability conditions enforced in the calculation and the quality of the approximate 3-RDM.

A computational study of radical initiated protein backbone homolytic dissociation on all natural amino acids.

Hydroxyl radical (˙OH) is known to be one of the most reactive species. In this work, the hydrogen abstraction by ˙OH from C and C atoms of all amino acids is studied in the framework of density functional theory as this is the most favorable reaction mechanism when this kind of radical attacks a protein. From the myriad routes that the oxidation of a protein by a ˙OH radical may follow, fragmentation of the protein is one of the most damaging ones as it hampers the normal function of the protein.

Separation of dynamic and nondynamic correlation.

The account of electron correlation and its efficient separation into dynamic and nondynamic parts plays a key role in the development of computational methods. In this paper we suggest a physically-sound matrix formulation to split electron correlation into dynamic and nondynamic parts using the two-particle cumulant matrix and a measure of the deviation from idempotency of the first-order density matrix. These matrices are applied to a two-electron model, giving rise to a simplified electron correlation index that (i) depends only on natural orbitals and their occupancies, (ii) can be straightforwardly decomposed into orbital contributions and (iii) splits into dynamic and nondynamic correlation parts that (iv) admit a local version.

Oxidation States from Wave Function Analysis.

We introduce a simple and general scheme to derive from wavefuntion analysis the most appropriate atomic/fragment electron configurations in a molecular system, from which oxidation states can be inferred. The method can be applied for any level of theory for which the first-order density matrix is available, and unlike others, it is not restricted to transition metal complexes. The method relies on the so-called spin-resolved effective atomic orbitals which for the present purpose is extended here to deal with molecular fragments/ligands.

H4: A challenging system for natural orbital functional approximations.

The correct description of nondynamic correlation by electronic structure methods not belonging to the multireference family is a challenging issue. The transition of D(2h) to D(4h) symmetry in H4 molecule is among the most simple archetypal examples to illustrate the consequences of missing nondynamic correlation effects. The resurgence of interest in density matrix functional methods has brought several new methods including the family of Piris Natural Orbital Functionals (PNOF).

Two new constraints for the cumulant matrix.

We suggest new strict constraints that the two-particle cumulant matrix should fulfill. The constraints are obtained from the decomposition of ⟨Ŝ(2)⟩, previously developed in our laboratory, and the vanishing number of electrons shared by two non-interacting fragments. The conditions impose stringent constraints into the cumulant structure without any need to perform an orbital optimization procedure thus carrying very small or no computational effort.

Diradical character from the local spin analysis.

Diradical species are analyzed in light of the local spin analysis. The atomic and diatomic contributions to the overall 〈Ŝ(2)〉 value are used to detect the diradical character of a number of molecular species mostly in their singlet state, for which no spin density exists. A general procedure for the quantification of diradical character for both singlet and triplet states is achieved by using a recently introduced index that measures the deviation of an actual molecule from an ideal system of perfectly localized spin centers.

Characterization and Quantification of Polyradical Character.

The decomposition of ⟨Ŝ(2)⟩ into atomic and diatomic contributions (local spin analysis) is used to detect and quantify the polyradical character of molecular systems. A model triradical system is studied in detail, and the local spin analysis is used to distinguish several patterns of local spin distributions and spin-spin interactions that can be found for different electronic states. How close a real molecular system is to an ideal system of k perfectly localized spin centers is utilized to define a measure of its k-radical character.

Local spin analysis and chemical bonding.

The electronic structure of main-group diatomic molecules is discussed in the light of local spin analysis. A deep investigation into the origin of local spins and their coupling is presented. It is shown that the presence of significant local spins in bonded molecules flags deviations from the classical bonding prototypes.