Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology

Persistence of atoms in molecules: there is room beyond electron densities

Evidence that the electronic structure of atoms persists in molecules to a much greater extent than has been usually admitted is presented. This is achieved by resorting to N-electron real-space descriptors instead of one- or at most two-particle projections like the electron or exchange-correlation densities. Here, the 3N-dimensional maxima of the square of the wavefunction, the so-called Born maxima, are used. Since this technique is relatively unknown to the crystallographic community, a case-based approach is taken, revisiting first the Born maxima of atoms in their ground state and then some of their excited states. It is shown how they survive in molecules and that, beyond any doubt, the distribution of electrons around an atom in a molecule can be recognized as that of its isolated, in many cases excited, counterpart, relating this fact with the concept of energetic promotion. Several other cases that exemplify the applicability of the technique to solve chemical bonding conflicts and to introduce predictability in real-space analyses are also examined.

The IQA Energy Partition in a Drug Design Setting: A Hepatitis C Virus RNA-Dependent RNA Polymerase (NS5B) Case Study

The interaction of the thumb site II of the NS5B protein of hepatitis C virus and a pair of drug candidates was studied using a topological energy decomposition method called interacting quantum atoms (IQA). The atomic energies were then processed by the relative energy gradient (REG) method, which extracts chemical insight by computation based on minimal assumptions. REG reveals the most important IQA energy contributions, by atom and energy type (electrostatics, sterics, and exchange–correlation), that are responsible for the behaviour of the whole system, systematically from a short-range ligand–pocket interaction until a distance of approximately 22 Å. The degree of covalency in various key interatomic interactions can be quantified. No exchange–correlation contribution is responsible for the changes in the energy profile of both pocket–ligand systems investigated in the ligand–pocket distances equal to or greater than that of the global minimum. Regarding the hydrogen bonds in the system, a “neighbour effect” was observed thanks to the REG method, which states that a carbon atom would rather not have its covalent neighbour oxygen form a hydrogen bond. The combination of IQA and REG enables the automatic identification of the pharmacophore in the ligands. The coarser Interacting Quantum Fragments (IQF) enables the determination of which amino acids of the pocket contribute most to the binding and the type of energy of said binding. This work is an example of the contribution topological energy decomposition methods can make to fragment-based drug design.

Localization and Delocalization in Solids from Electron Distribution Functions

The extent of electron localization and delocalization in molecular and condensed phases has been the subject of intense scrutiny over the years. In Chemistry, where real, instead of momentum space viewpoints are many times closer to intuition, a plethora of localization descriptors exist, including a family of indices invariant under orbital transformations that rely only on an underlying partition of the physical space into meaningful regions. These localization and delocalization indices measure the fluctuation of the electron population contained in such domains, and have been rigorously related to the insulating or conductive character of extended systems. Knowledge of the full electron population probability distribution function is also available in molecules, where it has provided many meaningful results as well as uncovered exotic interaction regimes in excited states. Electron distribution functions (EDFs), which can be seen as real space analogs of Pauling resonance structures, are now reported in periodic systems. In agreement with what is known in finite systems, ionic compounds display narrow EDFs that get wider as covalency sets in. Contrarily to conventional wisdom, most electrons delocalize over their nearest neighbors, even in quasi electron-gas metals like sodium, and it is only in the decay rate of the probability distribution where conductors and insulators can be distinguished.

Local spin and open quantum systems: clarifying misconceptions, unifying approaches

The theory of open quantum systems (OQSs) is applied to partition the squared spin operator into fragment (local spin) and interfragment (spin-coupling) contributions in a molecular system.

Reliability of HF/IQA, B3LYP/IQA, and MP2/IQA data in interpreting the nature and strength of interactions

Using CCSD/BBC1/IQA as a reference to describe interactions in glycol conformers, including O4⋯H6 and O3⋯O4 interactions, B3LYP/IQA data produced an exact qualitative picture and exceptionally reliable IQA energy changes, resulting in a perfectly comparable FAMSEC-based quantitative interpretation.

Decoding real space bonding descriptors in valence bond language

Real space bonding descriptors are orbital invariant indices that can be obtained independently of the theoretical framework used to compute a given wavefunction. Here we show how to use them to read in real space some widely used concepts in Valence Bond (VB) theory, such as ionic/covalent characters or covalent-ionic resonance energies. All of these are essential ingredients used when building VB chemical insight. Electron number distribution functions are employed to directly map ionic and covalent weights with real space delocalization indices. We show that covalency, understood as delocalization, emerges in position space from the fluctuation of electron populations. This is mapped in VB to covalent-ionic resonance. The reasons why this is not so in the standard language of non-orthogonal VB are examined. A simple real space ionic character index that maintains the essence of its VB equivalent is defined and examined in simple model systems. The conclusions of this work ease travelling among the sometimes conflicting molecular orbital, real space, and valence bond interpretations in chemical bonding theory.

An unexpected bridge between chemical bonding indicators and electrical conductivity through the localization tensor

While the modern theory of the insulating state shows that the conducting or insulating properties of a system can be extracted solely from the ground state properties via the so-called localization tensor (LT), no chemical reading of this important quantity has ever been offered. Here, a remarkable link between the LT and the bond orders as described by the delocalization indices (DIs) of chemical bonding theory is reported. This is achieved through a real space partition of the LT into intra- and interatomic contributions. We show that the convergence or divergence of the LT in the thermodynamic limit, which signals the insulating or conducting nature of an extended system, respectively, can be nailed down to DIs. This allows for the exploitation of traditional chemical intuition to identify essential and spectator atomic groups in determining electrical conductivity. The thermodynamic limit of the LT is controlled by the spatial decay rate of the interatomic DIs, exponential in insulators and power-law in conductors. Computational data of a few selected toy systems corroborate our results.

Extension of the interacting quantum atoms (IQA) approach to B3LYP level density functional theory (DFT)

An interaction between two atoms, bonded or non-bonded, consists of interatomic contributions: electrostatic energy, exchange energy and electronic correlation energy. Together with the intra-atomic energy of an atom, these contributions are the basic components of the Interacting Quantum Atom (IQA) energy decomposition scheme. Here, we investigate IQA's proper use in conjunction with an explicit implementation of the B3LYP functional. The recovery of the total molecular energy from the IQA components is emphasised, for the first time. A systematic study of three model systems of biological relevance, N-methylacetamide (NMA), the doubly capped tripeptide GlyGlyGly and an alloxan dimer, shows the stabilization effect of B3LYP on most of the interatomic exchange energies (V) compared to their Hartree-Fock values. Diagrams of exchange energies versus interatomic distance show the clustering of interactions, one cluster for each 1,n (n = 1 to 6 where the atoms are separated by n - 1 bonds). The positioning of some V values outside their expected cluster marks interesting interactions.

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective

Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (Oi-1 , Ci , Ni , Ni+1 ) and some sidechain hydrogen atoms (Hγ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the Oi-1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Reliability of interacting quantum atoms (IQA) data computed from post-HF densities: impact of the approximation used

The BBC1 approximation is recommended for IQA calculations; MP2/BBC1 and CCSD/BBC1 produced highly comparable FAMSEC-based interpretations of intramolecular interactions.

Decay Rate of Correlated Real-Space Delocalization Measures: Insights into Chemical Bonding and Mott Transitions from Hydrogen Chains

We study in this contribution the spatial decay rate of real-space localization and delocalization indices in correlated systems. To that end, we examine Hubbard and quantum chemical models of simple cyclic hydrogen chains, showing that all descriptors of delocalization converge quickly toward the infinite chain limits. It is then shown that the localization index may be understood as a generalization of the standard order parameter in Mott insulator transitions and that the origin of the enigmatic sigmoidal profile of delocalization indices in chemical bond-breaking processes lies in the nonlinear mapping between intersite distances and correlation parameters. Although the long-range asymptotic decay of delocalization indices is exponential, we show that as the correlation parameter decreases quantum mechanical interference sets in and a switch to an oscillating pattern, related to core chemical concepts such as resonance or mesomerism, appears.

Hydrogen bond cooperativity and anticooperativity within the water hexamer

We propose a hierarchy of H-bond strength in terms of the single and double character of the involved donor and acceptors within different structures of (H₂O)₆.

Atomic decomposition of conceptual DFT descriptors: application to proton transfer reactions

We present an atomic decomposition of the molecular energy, reaction force and reaction flux, which is based on Bader's atoms-in-molecules theory.

Performance of the density matrix functional theory in the quantum theory of atoms in molecules

The generalization to arbitrary molecular geometries of the energetic partitioning provided by the atomic virial theorem of the quantum theory of atoms in molecules (QTAIM) leads to an exact and chemically intuitive energy partitioning scheme, the interacting quantum atoms (IQA) approach, that depends on the availability of second-order reduced density matrices (2-RDMs). This work explores the performance of this approach in particular and of the QTAIM in general with approximate 2-RDMs obtained from the density matrix functional theory (DMFT), which rests on the natural expansion (natural orbitals and their corresponding occupation numbers) of the first-order reduced density matrix (1-RDM). A number of these functionals have been implemented in the promolden code and used to perform QTAIM and IQA analyses on several representative molecules and model chemical reactions. Total energies, covalent intra- and interbasin exchange-correlation interactions, as well as localization and delocalization indices have been determined with these functionals from 1-RDMs obtained at different levels of theory. Results are compared to the values computed from the exact 2-RDMs, whenever possible.

Nature of Chemical Interactions from the Profiles of Electron Delocalization Indices

We analyze the behavior of the profiles of delocalization indices (DIs) between relevant pairs of atoms along reaction coordinates for a set of model chemical processes. A relationship between the topology of the DI and the nature of the underlying chemical change is reported. As shown, exponential shapes correspond to the traditional category of repulsive/nonbonded interactions, while sigmoidal profiles signal the formation/breaking of chemical links.

Bond paths as privileged exchange channels

Evidence that the bond paths of the quantum theory of atoms-in-molecules (QTAIM) signal preferred quantum-mechanical exchange channels is presented. We show how bond paths between an atom A and the atoms B in its environment appear to be determined by competition among the A-B exchange-correlation energies that always contribute to stabilize the A-B interactions. These pairwise additive stabilizations depend neither on the attractive or repulsive nature of the classical electrostatic interaction between the atoms' charge densities, nor on the change in the self energies of the atoms involved. These other terms may well cause an overall molecular-energy increase in spite of a possibly large A-B exchange-correlation stabilization. After our proposal, bond paths, both at and out of equilibrium geometries, are endowed with a specific energetic meaning that should contribute to reconcile the orthodox QTAIM interpretation with other widely accepted views, and to settle recent controversies questioning the meaning of hydrogen-hydrogen bonding and the nature of the so-called "steric interactions", the role of bond paths in endohedral complexes, and the generality of the results provided by the QTAIM. Implications for the nature of more general closed-shell interactions are also briefly discussed.

Electron number probability distributions for correlated wave functions

Efficient formulas for computing the probability of finding exactly an integer number of electrons in an arbitrarily chosen volume are only known for single-determinant wave functions [E. Cances et al., Theor. Chem. Acc. 111, 373 (2004)]. In this article, an algebraic method is presented that extends these formulas to the case of multideterminant wave functions and any number of disjoint volumes. The derived expressions are applied to compute the probabilities within the atomic domains derived from the space partitioning based on the quantum theory of atoms in molecules. Results for a series of test molecules are presented, paying particular attention to the effects of electron correlation and of some numerical approximations on the computed probabilities.

Energy partitioning schemes

The paper gives an overview, generalization and systematization of the different energy decomposition schemes we have devised in the last few years by using both the 3-D analysis (the atoms are represented by different parts of the physical space) and the Hilbert space analysis in terms of the basis orbitals assigned to the individual atoms. The so called "atomic decomposition of identity" provides us the most general formalism for analyzing different physical quantities in terms of individual atoms or pairs of atoms. (The "atomic decomposition of identity" means that we present the identity operator as a sum of operators assigned to the individual atoms.) By proper definitions of the atomic operators, both Hilbert-space and the different 3-D decomposition schemes can be treated on an equal footing. Several different but closely related energy decomposition schemes have been proposed for the Hilbert space analysis. They differ by exact or approximate treatment of the three- and four-center integrals and by considering the kinetic energy as a part of the atomic Hamiltonian or as having genuine two-center components, too. (Also, some finite basis correction terms may be treated in different manners.) The exact schemes are obtained by using the "atomic decomposition of identity". In the approximate schemes a projective integral approximation is also introduced, thus the energy components contain only one- and two-center integrals. The diatomic energy contributions have also been decomposed into terms of different physical nature (electrostatic, exchange etc.) The 3-D analysis may be performed either in terms of disjunct atomic domains, as in the case of the AIM formalism, or by using the so called "fuzzy atoms" which do not have sharp boundaries but exhibit a continuous transition from one to another. The different schemes give different numbers, but each is capable of reflecting the most important intramolecular interactions as well as the secondary ones--e.g. intramolecular interactions of type C-H[...]O.