C5 Pentacle Structures: A Localization-Delocalization Matrices Approach.

This article explores the possible presence of a pentacle valence bond structure in C 5 ${_5 }$ cyclic molecules. At this end, we have used quantum chemistry tools to elucidate the possible arrangement and the nature of chemical bonds within linear, cyclic, and three-dimensional structures only formed by five carbon atoms. While the linear structure is clearly the most stable one, local minima were obtained for both bi- and three-dimensional structures. Using the localization-delocalization matrices approach, we characterize both the minimum linear structure and the cyclic ones. Interestingly, the linear structure is a combination of ionic and covalent bonds, albeit the four distances are almost identical, when using Density Functional Theory. For cyclic C 5 ${_5 }$ , the pentacle bonding arrangement emerges as a significant Lewis structure, indicative of an unusual formal configuration characterized by five intersecting C-C bonds. Our calculations show that this pentacle arrangement in cyclic C 5 ${_5 }$ scheme is also present in the more known cyclo-pentadienyl molecule.

Exploring the Reactivity of Donor-Acceptor Systems through a Combined Conceptual and Constrained DFT Approach.

In the context of the conceptual density functional theory (cDFT) and based on the computational efficiency of the constrained DFT (CDFT), we demonstrate that chemical reactivity can be governed by the difference between the local interacting chemical potentials of the reactants (referred as Edual), in agreement with Sanderson's equalization principle. In a proof-of-concept study, we investigated illustrative examples involving typical non-covalent donor-acceptor systems and reactive systems are provided. For the selected systems, our approach reveals significant mimicking between Edual and the DFT-computed intermolecular interaction energy profiles. We further evaluate the influence of the Coulomb and exchange-correlation contributions in Edual. These latter results suggest that numerous potential energy surfaces of clusters can be explored using a Sanderson-like model only based on classical interactions between molecular orbitals domains. To conclude, this study achieved a deeper understanding of the principles of cDFT and assessed, in a wider context, its efficiency in predicting the chemical reactivity.

Promising insights in parallel grid-based algorithms for quantum chemical topology.

Some straightforward improvements designed to make grid-based quantum chemical topology more efficient and faster are presented. The strategy focuses on both the evaluation of the scalar function over three-dimensional discrete grids and the algorithms aimed to follow and integrate gradient trajectories over the basin volumes together. Beyond the density analysis, we show that the scheme is quite suitable for the electron localization function and its complex topology. With this speed-up of the parallelized process used to generate 3d-grids, this new scheme is several orders of magnitude faster than the original grid-based method implemented in our laboratory (TopMod09). The efficiency of our implementation (TopChem2) was also compared with well-known grid-based algorithms designed to assign the grid points to basins. The performances, speed versus accuracy have been discussed on the basis of results obtained from selected illustrative examples.

Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding.

The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin-orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C-At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.

Exploring The Sequence of Electron Density Along The Chemical Reactions Between Carbonyl Oxides And Ammonia/Water Using Bond Evolution Theory.

The molecular mechanism of the reactions between four carbonyl oxides and ammonia/water are investigated using the M06-2X functional together with 6-311++G(d,p) basis set. The analysis of activation and reaction enthalpy shows that the exothermicity of each process increased with the substitution of electron donating substituents (methyl and ethenyl). Along each reaction pathway, two new chemical bonds C-N/C-O and O-H are expected to form. A detailed analysis of the flow of the electron density during their formation have been characterized from the perspective of bonding evolution theory (BET). For all reaction pathways, BET revealed that the process of C-N and O-H bond formation takes place within four structural stability domains (SSD), which can be summarized as follows: the depopulation of V(N) basin with the formation of first C-N bond (appearance of V(C,N) basin), cleavage of N-H bond with the creation of V(N) and V(H) monosynaptic basin, and finally the V(H,O) disynaptic basin related to O-H bond. On the other hand, in the case of water, the cleavage of O-H bond with the formation of V(O) and V(H) basins is the first stage, followed by the formation of the O-H bond as a second stage, and finally the creation of C-O bond.

The Topological Analysis of the ELFx Localization Function: Quantitative Prediction of Hydrogen Bonds in the Guanine-Cytosine Pair.

In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) -cytosine (C) pair, we successfully predict the best orientation between the base pairs held together by hydrogen bonds and leading to the formation of the typical Watson Crick structure of the GC pair. Beyond the global minimum, some local stationary points of the targeted pair are also clearly identified.

New insights in chemical reactivity from quantum chemical topology.

Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

Triggering Electron Transfer in Co(I) Dimers: Computational Evidences for a Reversible Disproportionation Mechanism.

An inner-sphere disproportionation mechanism of the Co(I) precursor CoCl(PPh3 )3 is described through a Density Functional Theory study. The essential role of oleylamine in this process is unravelled. A detailed analysis of the electronic structure of Cobalt dimers of the general formula Co2 Cl2 Ln (L=NH3 and PH3 ) demonstrates that electron transfer is triggered by asymetric coordination of amine and phosphine to stabilize a mixed-valence Co(II)-Co(0) dimer. This is consistent with the HSAB statement that both amine and phosphine ligands are required to stabilize the reaction products, respectively Co(II) and Co(0) centers. We propose a quasi-athermic multi-step disproportionation mechanism with low activation barriers where the electron transfer goes through simple ligand exchanges between Co.

Quantum chemical topology at the spin-orbit configuration interaction level: Application to astatine compounds.

We report a methodology that allows the investigation of the consequences of the spin-orbit coupling by means of the QTAIM and ELF topological analyses performed on top of relativistic and multiconfigurational wave functions. In practice, it relies on the "state-specific" natural orbitals (NOs; expressed in a Cartesian Gaussian-type orbital basis) and their occupation numbers (ONs) for the quantum state of interest, arising from a spin-orbit configuration interaction calculation. The ground states of astatine diatomic molecules (AtX with X = AtF) and trihalide anions (IAtI- , BrAtBr- , and IAtBr- ) are studied, at exact two-component relativistic coupled cluster geometries, revealing unusual topological properties as well as a significant role of the spin-orbit coupling on these. In essence, the presented methodology can also be applied to the ground and/or excited states of any compound, with controlled validity up to including elements with active 5d, 6p, and/or 5f shells, and potential limitations starting with active 6d, 7p, and/or 6f shells bearing strong spin-orbit couplings.

Crystallographic structure and crystal field parameters in the [AnIV(DPA)3]2- series, An = Th, U, Np, Pu.

The [AnIV(DPA)3]2- series with An = Th, U, Np, Pu has been synthesized and characterized using SC-XRD and vibrational spectroscopy. First principles calculations were performed, the total electron density is analyzed using the Quantum Theory of Atoms in Molecules. Crystal field parameters and strength parameters are deduced following a previous work on the LnIII analog series e.g. [J. Jung et al., Chem. - Eur. J., 2019, 25, 15112]. The trends in the parameters along the series are compared to the LnIII complexes. They evidence larger covalent interactions and larger J mixing.

Quantum chemical topology from tight augmented core densities.

Based on parametrized tight Gaussian functions, an efficient and robust methodology designed to restore the effective core potentials electron densities and the inner shells of the electron localization function is introduced and tested. Attention is focused on the underlying effects of augmented coreless electron densities on selected quantum topological descriptors computed for a test set of species containing heavy elements such as the emblematic uranyl cation. Also, this article shows how a proper topology of the electron density can be recovered from semi-empirical Hückel calculations where core densities are missing.

On the Interplay between Charge-Shift Bonding and Halogen Bonding.

The nature of halogen-bond interactions has been analysed from the perspective of the astatine element, which is potentially the strongest halogen-bond donor. Relativistic quantum calculations on complexes formed between halide anions and a series of Y3 C-X (Y=F to X, X=I, At) halogen-bond donors disclosed unexpected trends, e. g., At3 C-At revealing a weaker donating ability than I3 C-I despite a stronger polarizability. All the observed peculiarities have their origin in a specific component of C-Y bonds: the charge-shift bonding. Descriptors of the Quantum Chemical Topology show that the halogen-bond strength can be quantitatively anticipated from the magnitude of charge-shift bonding operating in Y3 C-X. The charge-shift mechanism weakens the ability of the halogen atom X to engage in halogen bonds. This outcome provides rationales for outlier halogen-bond complexes, which are at variance with the consensus that the halogen-bond strength scales with the polarizability of the halogen atom.

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.

Spin-orbit coupling as a probe to decipher halogen bonding.

The nature of halogen-bond interactions is scrutinized from the perspective of astatine, the heaviest halogen element. Potentially the strongest halogen-bond donor, its ability is shown to be deeply affected by relativistic effects and especially by the spin-orbit coupling. Complexes between a series of XY dihalogens (X, Y = At, I, Br, Cl and F) and ammonia are studied with two-component relativistic quantum calculations, revealing that the spin-orbit interaction leads to a weaker halogen-bond donating ability of the diastatine species with respect to diiodine. In addition, the donating ability of the lighter halogen elements, iodine and bromine, in the AtI and AtBr species is more decreased by the spin-orbit coupling than that of astatine. This can only be rationalized from the evolution of a charge-transfer descriptor, the local electrophilicity ω+S,max, determined for the pre-reactive XY species. Finally, the investigation of the spin-orbit coupling effects by means of quantum chemical topology methods allows us to unveil the connection between the astatine propensity to form charge-shift bonds and the astatine ability to engage in halogen bonds.

Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics.

We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.

The bonding picture in hypervalent XF3 (X = Cl, Br, I, At) fluorides revisited with quantum chemical topology.

Hypervalent XF3 (X = Cl, Br, I, At) fluorides exhibit T-shaped C2V equilibrium structures with the heavier of them, AtF3 , also revealing an almost isoenergetic planar D3h structure. Factors explaining this behavior based on simple "chemical intuition" are currently missing. In this work, we combine non-relativistic (ClF3 ), scalar-relativistic and two-component (X = Br - At) density functional theory calculations, and bonding analyses based on the electron localization function and the quantum theory of atoms in molecules. Typical signatures of charge-shift bonding have been identified at the bent T-shaped structures of ClF3 and BrF3 , while the bonds of the other structures exhibit a dominant ionic character. With the aim of explaining the D3h structure of AtF3 , we extend the multipole expansion analysis to the framework of two-component single-reference calculations. This methodological advance enables us to rationalize the relative stability of the T-shaped C2v and the planar D3h structures: the Coulomb repulsions between the two lone-pairs of the central atom and between each lone-pair and each fluorine ligand are found significantly larger at the D3h structures than at the C2v ones for X = Cl - I, but not with X = At. This comes with the increasing stabilization, along the XF3 series, of the planar D3h structure with respect to the global T-shaped C2v minima. Hence, we show that the careful use of principles that are at the heart of the valence shell electron pair repulsion model provides reasonable justifications for stable planar D3h structures in AX3 E2 systems. © 2017 Wiley Periodicals, Inc.

Electron localization function from density components.

This work addresses the decomposition of the Electron Localization Function (ELF) into partial density contributions using an appealing split of kinetic energy densities. Regarding the degree of the electron localization, the relationship between ELF and its usual spin-polarized formula is discussed. A new polarized ELF formula, built from any subsystems of the density, and a localization function, quantifying the measure of electron localization for only a subpart of the total system are introduced. The methodology appears tailored to describe the electron localization in bonding patterns of subsystems, such as the local nucleophilic character. Beyond these striking examples, this work opens up opportunities to describe any electronic properties that depend only on subparts of the density in atoms, molecules, or solids. © 2016 Wiley Periodicals, Inc.

(211)At-labeled agents for alpha-immunotherapy: On the in vivo stability of astatine-agent bonds.

The application of (211)At to targeted cancer therapy is currently hindered by the rapid deastatination that occurs in vivo. As the deastatination mechanism is unknown, we tackled this issue from the viewpoint of the intrinsic properties of At-involving chemical bonds. An apparent correlation has been evidenced between in vivo stability of (211)At-labeled compounds and the At-R (R = C, B) bond enthalpies obtained from relativistic quantum mechanical calculations. Furthermore, we highlight important differences in the nature of the At-C and At-B bonds of interest, e.g. the opposite signs of the effective astatine charges, which implies different stabilities with respect to the biological medium. Beyond their practical use for rationalizing the labeling protocols used for (211)At, the proposed computational approach can readily be used to investigate bioactive molecules labeled with other heavy radionuclides.

Electronic structures and geometries of the XF3 (X = Cl, Br, I, At) fluorides.

The potential energy surfaces of the group 17 XF3 (X = Cl, Br, I, At) fluorides have been investigated for the first time with multiconfigurational wave function theory approaches. In agreement with experiment, bent T-shaped C(2v) structures are computed for ClF3, BrF3, and IF3, while we predict that an average D(3h) structure would be experimentally observed for AtF3. Electron correlation and scalar relativistic effects strongly reduce the energy difference between the D(3h) geometry and the C(2v) one, along the XF3 series, and in the X = At case, spin-orbit coupling also slightly reduces this energy difference. AtF3 is a borderline system where the D(3h) structure becomes a minimum, i.e., the pseudo-Jahn-Teller effect is inhibited since electron correlation and scalar-relativistic effects create small energy barriers leading to the global C(2v) minima, although both types of effects interfere.

Toward an Understanding of the Oxidation Process of Methionine Enkephalin: A Combined Electrochemistry, Quantum Chemistry and Quantum Chemical Topology Analysis.

Recent experimental results about the oxidation of methionine enkephalin by ·OH radicals indicated an intramolecular electron transfer between the C-terminal methionine radical cation and the tyrosine N-terminus too fast to be observed. We have investigated the thermodynamic possibility of this intramolecular electron transfer by calculating the one-electron redox potentials of both residues for several conformations of the peptide, extracted from the experimental data of the Protein Data Bank (1PLW). Using a QM/MM approach, we show that the redox potential of the Met(•+)/Met couple is higher than that of the TyrOH(•+)/TyrOH one (tyrosine is denoted as TyrOH) for all conformations. The intramolecular electron transfer between both residues (from TyrOH to Met(•+)) is thus always thermodynamically allowed. Previously, we had performed topological studies on the intramolecular electron transfer which predicted this charge transfer. A study by cyclic voltammetry pointed out that the wave belonging to methionine is not present when methionine enkephalin is oxidized and only the direct involvement of the tyrosine residue is observed.