New insights in quantum chemical topology studies using numerical grid-based analyses

Anomalous π-backbonding in complexes between B(SiR3)3 and N2: catalytic activation and breaking of scaling relations

Chemical transformations of molecular nitrogen (N2), including the nitrogen reduction reaction (NRR), are difficult to catalyze because of the weak Lewis basicity of N2. In this study, it is shown that Lewis acids of the types B(SiR3)3 and B(GeR3)3 bind N2 and CO with anomalously short and strong B-N or B-C bonds. B(SiH3)3·N2 has a B-N bond length of 1.48 Å and a complexation enthalpy of -15.9 kcal mol-1 at the M06-2X/jun-cc-pVTZ level. The selective binding enhancement of N2 and CO is due to π-backbonding from Lewis acid to Lewis base, as demonstrated by orbital analysis and density difference plots. The π-backbonding is found to be a consequence of constructive orbital interactions between the diffuse and highly polarizable B-Si and B-Ge bond regions and the π and π* orbitals of N2. This interaction is strengthened by electron donating substituents on Si or Ge. The π-backbonding interaction is predicted to activate N2 for chemical transformation and reduction, as it decreases the electron density and increases the length of the N-N bond. The binding of N2 and CO by the B(SiR3)3 and B(GeR3)3 types of Lewis acids also has a strong σ-bonding contribution. The relatively high σ-bond strength is connected to the highly positive surface electrostatic potential [VS(r)] above the B atom in the tetragonal binding conformation, but the σ-bonding also has a significant coordinate covalent (dative) contribution. Electron withdrawing substituents increase the potential and the σ-bond strength, but favor the binding of regular Lewis acids, such as NH3 and F-, more strongly than binding of N2 and CO. Molecules of the types B(SiR3)3 and B(GeR3)3 are chemically labile and difficult to synthesize. Heterogenous catalysts with the wanted B(Si-)3 or B(Ge-)3 bonding motif may be prepared by boron doping of nanostructured silicon or germanium compounds. B-doped and hydrogenated silicene is found to have promising properties as catalyst for the electrochemical NRR.

TopIso3D Viewer: Enhancing Topological Analysis through 3D Isosurfaces

We present TopIso3D Viewer, a software with a user-friendly graphical interface, that generates three-dimensional maps to analyze descriptors based on the Quantum Theory of Atoms in Molecules (QTAIM), applied in periodic and nonperiodic systems. The software also automates the launching of topological analysis calculations through the Topond package and generates a report that facilitates the identification of the values of the calculated descriptors, in the Bond Critical Points (BCP) and Critical Points of the Laplacian of the electron density (LCP), facilitating the classification of chemical interactions. The map projects created can be stored in the form of HTML files, for later consultation through any type of browser. For validation of the software, several systems with 0-3D dimensions were studied. In addition, the topology of urea molecular crystal and its isolated molecule were revisited.

Relativistic Effects Stabilize Unusual Gold(II) Sulfate Structure via Aurophilic Interactions

The crystal structure of gold(II) sulfate is strikingly different from other coinage metal(II) sulfates. Central to the unsual AuSO₄ bulk structure is the Au₂⁴⁺ ion with a very close Au-Au contact, which is a structural feature that does not appear in CuSO₄ and AgSO₄. To shed some light on this unusual behavior, we decided to investigate the relative stabilities of the coinage metal(II) sulfates utilizing periodic Density Functional Theory. By computing relative energies of the hypothetical nonrelativistic gold(II) sulfate (Au_NRSO₄) in different structural arrangements and performing chemical bonding analyses employing the Electron Localization Function as well as the Quantum Theory of Atoms in Molecules method, we show that the stability of the unsual AuSO₄ bulk structure can be related to aurophilic interactions enabled by relativistic effects. From the relative stabilities and UV-vis spectra computed via GW methodology, we predict that Au_NRSO₄ would assume the structure of either copper(II) sulfate or silver(II) sulfate with almost equal likelihood and appear as bright-violet or deep-blue substances, respectively.

Template Synthesis of NPN' Pincer-type Ligands at Titanium Using an Ambiphilic Phosphide Scaffold

Ti-imido complex [TiCl(N^tBu)(BIPP)] [1; BIPP = bis(iminophosphoranyl)phosphide ligand] reacts with terminal alkynes R-C≡CH (R = phenyl, isopropenyl, cyclopropyl, and 2-pyridyl) via P-P bond cleavage of the BIPP ligand. The resulting complexes [TiCl(NPN')(NPhPPh₂)] (2a-d) contain a pincer-type NPN' phosphide ligand that incorporates the terminal alkyne and the imido ligand from complex 1. Complexes 2a-d feature two chiral centers (Ti and P) with interdependent absolute configurations; thus, they are formed stereoselectively. Complex 2a (R = phenyl) undergoes chloride abstraction with [Et₃SiHSiEt₃][B(C₆F₅)₄], yielding [Ti(NPN')(NPhPPh₂)][B(C₆F₅)₄] (3). Complex 3 is a moderately active and stereoselective initiator for the ring-opening polymerization of rac-lactide. Complex 3 activates the C═O bond of 4-iodobenzaldehyde to give complex 4 as a single diastereomer despite the presence of three chiral centers. Complex 3 undergoes transmetallation with SbCl₃, yielding [Sb(NPN')][B(C₆F₅)₄] (5) and [TiCl₃(NPhPPh₂)] (6) selectively. The bonding situation in 3 and 5 was analyzed using Bader's atoms in molecules and the electron localization function, showing that the nitrogen atoms of the NPN' ligand are electronically similar, and that the metal-phosphide interaction is more polar in the case of titanium.

LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis

The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.

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.

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 L_n (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.

New insights in chemical reactivity from quantum chemical topology

Based on the quantum chemical topology of the modified electron localization function ELF_x , 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 E_dual 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.

Reappraising Schmidpeter's bis(iminophosphoranyl)phosphides: coordination to transition metals and bonding analysis

The synthesis and characterization of a range of bis(iminophosphoranyl)phosphide (BIPP) group 4 and coinage metals complexes is reported. BIPP ligands bind group 4 metals in a pseudo fac-fashion, and the central phosphorus atom enables the formation of d⁰–d¹⁰ heterobimetallic complexes. Various DFT computational tools (including AIM, ELF and NCI) show that the phosphorus–metal interaction is either electrostatic (Ti) or dative (Au, Cu). A bridged homobimetallic Cu–Cu complex was also prepared and its spectroscopic properties were investigated. The theoretical analysis of the P–P bond in BIPP complexes reveals that (i) BIPP are closely related to ambiphilic triphosphenium (TP) cations; (ii) the P–P bonds are normal covalent (i.e. not dative) in both BIPP and TP.

The synthesis, characterization and computational analysis of a range of bis(iminophosphoranyl)phosphide (BIPP) group 4 and coinage metals complexes is reported. White phosphorus was used to install the central phosphorus atom.

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.

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

The [An^IV(DPA)₃]²⁻ series with An = Th, U, Np, Pu has been synthesized and characterized using SC-XRD, vibrational spectroscopy, and first principles calculations.

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.

Curly arrows, electron flow, and reaction mechanisms from the perspective of the bonding evolution theory

Despite the usefulness of curly arrows in chemistry, their relationship with real electron density flows is still imprecise, and even their direct connection to quantum chemistry is still controversial. The paradigmatic description - from first principles - of the mechanistic aspects of a given chemical process is based mainly on the relative energies and geometrical changes at the stationary points of the potential energy surface along the reaction pathway; however, it is not sufficient to describe chemical systems in terms of bonding aspects. Probing the electron density distribution during a chemical reaction can provide important insights, enabling us to understand and control chemical reactions. This aim has required an extension of the relationships between the concepts of traditional chemistry and those of quantum mechanics. Bonding evolution theory (BET), which combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT), provides a powerful method that offers insight into the molecular mechanism of chemical rearrangements. In agreement with the laws of physical and aspects of quantum theory, BET can be considered an appropriate tool to tackle chemical reactivity with a wide range of possible applications. In this work, BET is applied to address a long-standing problem: the ability to monitor the flow of electron density. BET analysis shows a connection between quantum mechanics and bond making/forming processes. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds and provides detailed physical grounds for this type of representation. We demonstrate this procedure using the test set of prototypical examples of thermal ring apertures, and the degenerated Cope rearrangement of semibullvalene.

Understanding the CO Dissociation in [Fe(CN)2(CO)2(dithiolate)]2- Complexes with Quantum Chemical Topology Tools

The active site of the [NiFe]-hydrogenase contains a pentacoordinated iron atom; therefore, a vacant coordination site is available for substrate binding. Nonetheless, most organometallic models of the [NiFe]-hydrogenase failed to reproduce this key feature of the active site. In order to rationalize such behavior, quantum chemical calculations were carried out on a series of [Fe(CN)₂(CO)_n(dithiolate)]^2- n = 1,2 complexes, where dithiolate denotes the ligands (CF₃)₂C₂S₂^2-, (CO₂Me)₂C₂S₂^2-, Ph₂C₂S₂^2-, C₆Cl₂H₂S₂^2-, C₆H₄S₂^2-, C₂H₄S₂^2-, and C₃H₆S₂^2-. Structural and energetic features are discussed, and a topological analysis based on two scalar fields, the one-electron density and the electron localization function (ELF), has been attempted to describe the nature of the metal-ligand bonds. The present approach contributes to better understand the ability of noninnocent dithiolene to strongly labilize one CO whereas innocent dithiolate cannot. The methodology developed throughout the paper could be useful in the field of the CO-releasing molecules.

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 C_2V equilibrium structures with the heavier of them, AtF₃ , also revealing an almost isoenergetic planar D_3h 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 D_3h 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 C_2v and the planar D_3h 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 D_3h structures than at the C_2v ones for X = Cl - I, but not with X = At. This comes with the increasing stabilization, along the XF₃ series, of the planar D_3h structure with respect to the global T-shaped C_2v 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 D_3h 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.

GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments

Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 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.

Structure of cobalt protoporphyrin chloride and its dimer, observation and DFT modeling

In this article we present a joint study by using time-of-flight mass spectroscopy and density functional theory of cobalt protoporphyrin dimer complexes.

Curly arrows meet electron density transfers in chemical reaction mechanisms: from electron localization function (ELF) analysis to valence-shell electron-pair repulsion (VSEPR) inspired interpretation

The displacement of the nuclei along the reaction path provides an explanatory interpretation of the electron density transfers making possible to understand chemical reactions.

Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin

We have studied electron transfers (ET) between electron donors and acceptors, taking as illustrative example the case of ET in methionine enkephalin. Recent pulse and gamma radiolysis experiments suggested that an ultrafast ET takes place from the C-terminal tyrosine residue to the N-terminal, oxidized, methionine residue. According to standard theoretical frameworks like the Marcus theory, ET can be decomposed into two successive steps: i) the achievement through thermal fluctuations, of a set of nuclear coordinates associated with degeneracy of the two electronic states, ii) the electron tunneling from the donor molecular orbital to the acceptor molecular orbital. Here, we focus on the analysis of the time-dependent electronic dynamics during the tunneling event. This is done by extending the approaches based on the topological analyses of stationary electronic density and of the electron localization function (ELF) to the time-dependent domain. Furthermore, we analyzed isosurfaces of the divergence of the current density, showing the paths that are followed by the tunneling electron from the donor to the acceptor. We show how these functions can be calculated with constrained density functional theory. Beyond this work, the topological tools used here can open up new opportunities for the electronic description in the time-dependent domain.