QTAIM and ETS-NOCV Analyses of Intramolecular CH···HC Interactions in Metal Complexes

Explaining the High Catalytic Activity in Bis(indenyl)methyl Zirconium Cation Using Combined EDA-NOCV/QTAIM Approach

The main purpose of this study is to elucidate some discrepancies already observed in the catalytic activity values of some zirconocene methyl cations. The EDA-NOCV scheme was employed for a theoretical description of the interactions between an ethylene molecule and five catalysts of zirconocene methyl cation. The nature of the chemical interactions has been elucidated through the QTAIM topological analysis. The steric hindrance due to the ligands was evaluated qualitatively by means of an IRI-based analysis and quantitively through Fisher information. The findings prove that the indenyl ligand seems to favor the orbital interaction between the ethylene molecule and the metal centre of zirconocene methyl cation. Both electrostatic and orbital contributions play a crucial role in stabilising the studied complexes. Based on the NOCV deformation density contributions, the strongest orbital interaction is reached with the bis(indenyl)methyl zirconium cation, which is the only one exhibiting covalent interactions. Especially, the strong contribution of π-back donation (occurring from the occupied orbitals of the zirconium atom to the π* anti-bonding orbital of ethylene) may be a key to understand why this catalyst has a higher polymerisation yield than the other studied catalysts. This work suggests a perspective for predicting values of catalytic activity when theoretically designing novel catalysts of zirconocene type.

Coordination polymers fabricated from Cd(NO3)2 and N,N′,O-pincer-type isonicotinoylhydrazone-based polytopic ligands – an insight from experimental and theoretical investigations

Three new Cd(ii) coordination polymers based on isonicotinohydrazide ligands (HLI, HLII) differing in the presence of a methyl unit have been obtained and extensively characterized by experimental and computational approaches.

Structural versatility of the quasi-aromatic Möbius type zinc(ii)-pseudohalide complexes – experimental and theoretical investigations

In this contribution we report for the first time fabrication, isolation, structural and theoretical characterization of the quasi-aromatic Möbius complexes [Zn(NCS)₂L^I] (1), [Zn₂(μ_1,1-N₃)₂(L^I)₂][ZnCl₃(MeOH)]₂·6MeOH (2) and [Zn(NCS)L^II]₂[Zn(NCS)₄]·MeOH (3), constructed from 1,2-diphenyl-1,2-bis((phenyl(pyridin-2-yl)methylene)hydrazono)ethane (L^I) or benzilbis(acetylpyridin-2-yl)methylidenehydrazone (L^II), respectively, and ZnCl₂ mixed with NH₄NCS or NaN₃. Structures 1–3 are dictated by both the bulkiness of the organic ligand and the nature of the inorganic counter ion. As evidenced from single crystal X-ray diffraction data species 1 has a neutral discrete heteroleptic mononuclear structure, whereas, complexes 2 and 3 exhibit a salt-like structure. Each structure contains a Zn^II atom chelated by one tetradentate twisted ligand L^I creating the unusual Möbius type topology. Theoretical investigations based on the EDDB method allowed us to determine that it constitutes the quasi-aromatic Möbius motif where a metal only induces the π-delocalization solely within the ligand part: 2.44|e| in 3, 3.14|e| in 2 and 3.44|e| in 1. It is found, that the degree of quasi-aromatic π-delocalization in the case of zinc species is significantly weaker (by ∼50%) than the corresponding estimations for cadmium systems – it is associated with the Zn–N bonds being more polar than the related Cd–N connections. The ETS-NOCV showed, that the monomers in 1 are bonded primarily through London dispersion forces, whereas long-range electrostatic stabilization is crucial in 2 and 3. A number of non-covalent interactions are additionally identified in the lattices of 1–3.

Interplay between various types of non-covalent interactions allowed for isolation of rare examples of Zn(ii) based quasi-aromatic Möbius type species.

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.

Interpretation of Tolman electronic parameters in the light of natural orbitals for chemical valence

Understanding the nature and the strength of metal-ligand interactions in d- and f-block metal complexes has always been a central issue for both synthetic and theoretical chemists. These interactions are usually described according to the well accepted Dewar-Chatt-Duncanson model, and thus over the years numerous research groups directed their efforts to shed light on the role of σ- and π-contributions. Among others, the electronic parameter introduced by Tolman in the 1970s represents a milestone in this field. Herein we present a quantitative description of the nickel-phosphine bond in Tolman's nickel(0) carbonyl complexes. The combination of Natural Orbitals for Chemical Valence with Energy Decomposition Analysis resulted in the definition of a new parameter (T^phos) which comprises all the energetic contributions needed to describe the nickel-phosphine bond and thus stands as a reliable descriptor of the electronic properties of phosphines. Moreover, steric effects of phosphines (i.e. Tolman's cone angles) have been considered too, and a linear relation including Ni-P bond distances, T^phos and cone angle has been found.

Structure and Electronic Properties of Unnatural Base Pairs: The Role of Dispersion Interactions

Recent reports of the successful incorporation of unnatural base pairs (UBPs), such as d5SICS-dNaM, in the gene sequence and replication with DNA is an important milestone in synthetic biology. Followed by this, several other UBPs, such as dTPT3-dNaM, dTPT3-dFIMO, dTPT3-IMO, dTPT3-FEMO, FTPT3-NaM, FTPT3-FIMO, FTPT3-IMO, and FTPT3-FEMO, have demonstrated similar or better retention and fidelity inside cells. Of these base pairs, dNaM-dTPT3 has been optimized to be a better fit inside a pAIO plasmid. Based on both implicit and explicit dispersion-corrected density functional theory (DFT) calculations, we show that although this set of UBPs is significantly diverse in elemental and structural configuration, the members do share a common trait of favoring a slipped parallel stacked dimer arrangement. Unlike the natural bases (A, T, G, C, and U), this set of UBPs has a negligible affinity for a Watson-Crick (WC)-type planar structure because they are invariably more stable within slipped parallel stacked orientations. We also observed that all the UBPs have either similar or higher binding energies with the natural bases in similar stacked orientations. When arranged between two natural base pairs, the UBPs exhibited a binding energy similar to that of three-base sequences of natural bases. Our computational data show that the most promising base pairs are 5SICS-NaM, TPT3-NaM, and TPT3-FEMO. These results are consistent with recent progress on experimental research into UBPs along with our previous calculations on the d5SICS-dNaM pair and, therefore, strengthen the hypothesis that hydrogen bonding might not be absolutely essential and that interbase stacking dispersion interactions play a key role in the stabilization of genetic materials.

Exploring Ultrashort Hydrogen-Hydrogen Nonbonded Contacts in Constrained Molecular Cavities

Confined molecular chambers such as macrocycle bridged E₁-H···H-E₂ (E₁(E₂) = Si(Si), 1) exhibit rare ultrashort H···H nonbonded contacts (d(H···H) = 1.56 Å). In this article, on the basis of density functional theory and ab initio molecular dynamics simulations, we propose new molecular motifs where d(H···H) can be reduced to 1.44 Å (E₁(E₂) = Si(Ge), 3). Further tuning the structure of the macrocycle by replacing the bulky phenyl groups by ethylenic spacers and substitution of the H-atoms by -CN groups makes the cavity more compact and furnishes even shorter d(H···H) = 1.38 Å (E₁(E₂) = Ge(Ge), 8). These unusually close H···H nonbonded contacts originate from the strong attractive noncovalent interactions between them, which are evident from various computational indicators, namely, NCI, Wiberg bond index, relaxed force constant, quantum theory of atoms in molecules, and natural orbitals for chemical valence combined with the extended transition state method analyses. Substantial stabilization of the in,in-configuration (exhibiting short H···H contacts) compared with the out,out-configuration (by ∼5.7 kcal/mol) and statistically insignificant fluctuations in ⟨d(H···H)⟩ and ⟨θ_av⟩(θ(E₁(E₂)-H···H = 152°) at room temperature confirm that the ultrashort H···H distances in these molecules are thermodynamically stable and would be persistent under ambient experimental conditions.

On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes

In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.

Formation of β-cyclodextrin complexes in an anhydrous environment

The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host-guest complexes and shows that hydrophobic interactions play a secondary role in this case. Graphical abstract The formation of complexes of β-cyclodextrin with selected n-alkanes, polyaromatics, and organic acids in an anhydrous environment is studied by differential scanning calorimetry, IR spectroscopy, and molecular modeling. The results obtained confirm the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds and give a new perspective on the mechanism of formation of host-guest complexes.

Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be(II) complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid

A method designed to investigate, on a fundamental level, the origin of relative stability of molecular systems using Be(II) complexes with nitrilotriacetic acid (NTA) and nitrilotri-3-propionic acid (NTPA) is described. It makes use of the primary and molecular fragment energy terms as defined in the IQA/F (Interacting Quantum Atoms/Fragments) framework. An extensive classical-type investigation, focused on single descriptors (bond length, density at critical point, the size of metal ion or coordination ring, interaction energy between Be(II) and a donor atom, etc.) showed that it is not possible to explain the experimental trend. The proposed methodology is fundamentally different in that it accounts for the total energy contributions coming from all atoms of selected molecular fragments, and monitors changes in defined energy terms (e.g., fragment deformation, inter- and intra-fragment interaction) on complex formation. By decomposing combined energy terms we identified the origin of relative stability of Be(II) (NTA) and Be(II) (NTPA) complexes. We found that the sum of coordination bonds' strength, as measured by interaction energies between Be(II) ion and donor atoms, favours Be(II) (NTA) but the binding energy of Be(II) ion to the entire ligand correlates well with experimental trend. Surprisingly, the origin of Be(II) (NTPA) being more stable is due to less severe repulsive interactions with the backbone of NTPA (C and H-atoms). This general purpose protocol can be employed not only to investigate the origin of relative stability of any molecular system (e.g., metal complexes) but, in principle, can be used as a predictive tool for, e.g., explaining reaction mechanism. © 2016 Wiley Periodicals, Inc.

Metal-interacted histidine dimer: an ETS-NOCV and XANES study

We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).

Fundamental relation between molecular geometry and real-space topology. Combined AIM, ELI-D, and ASF analysis of hapticities and intramolecular hydrogen-hydrogen bonds in zincocene-related compounds

Despite numerous advanced and widely distributed bonding theories such as MO, VB, NBO, AIM, and ELF/ELI-D, complex modes of bonding such as M-Cp*((R)) interactions (hapticities) in asymmetrical metallocenes or weak intramolecular interactions (e.g., hydrogen-hydrogen (H···H) bonds) still remain a challenge for these theories in terms of defining whether or not an atom-atom interaction line (a "chemical bond") should be drawn. In this work the intramolecular Zn-C(Cp*(R)) (R = Me, -(CH2)2NMe2, and -(CH2)3NMe2) and H···H connectivity of a systematic set of 12 zincocene-related compounds is analyzed in terms of AIM and ELI-D topology combined with the recently introduced aspherical stockholder fragment (ASF) surfaces. This computational analysis unravels a distinct dependency of the AIM and ELI-D topology against the molecular geometry for both types of interactions, which confirms and extends earlier findings on smaller sets of compounds. According to these results the complete real-space topology including strong, medium, and weak interactions of very large compounds such as proteins may be reliably predicted by sole inspection of accurately determined molecular geometries, which would on the one hand afford new applications (e.g., accurate estimation of numbers, types, and strengths of intra- and intermolecular interactions) and on the other hand have deep implications on the significance of the method.

Ruthenium(ii) complexes of N-heterocyclic carbenes derived from imidazolium-linked cyclophanes

Metal–ligand bonds in ruthenium(ii) complexes of N-heterocyclic carbenes derived from imidazolium-linked cyclophanes with a remarkable covalent character are shown.

Forced bonding and QTAIM deficiencies: a case study of the nature of interactions in He@adamantane and the origin of the high metastability

Calculations within the framework of the interacting quantum atoms (IQA) approach have shown that the interactions of the helium atom with both tertiary, tC, and secondary, sC, carbon atoms in the metastable He@adamantane (He@adam) endohedral complex are bonding in nature, whereas the earlier study performed within the framework of Bader's quantum theory of atoms in molecules (QTAIM) revealed that only He---tC interactions are bonding. The He---tC and He---sC bonding interactions are shown to be forced by the high pressure that the helium and carbon atoms exert upon each other in He@adam. The occurrence of a bonding interaction between the helium and sC atoms, which are not linked by a bond path, clearly shows that the lack of a bond path between two atoms does not necessarily indicate the lack of a bonding interaction, as is asserted by QTAIM. IQA calculations showed that not only the destabilization of the adamantane cage, but also a huge internal destabilization of the helium atom, contribute to the metastability of He@adam, these contributions being roughly equal. This result disproves previous opinions based on QTAIM analysis that only the destabilization of the adamantane cage accounts for the endothermicity of He@adam. Also, it was found that there is no homeomorphism of the ρ(r) and -v(r) fields of He@adam. Comparison of the IQA and QTAIM results on the interactions in He@adam exposes other deficiencies of the QTAIM approach. The reasons for the deficiencies in the QTAIM approach are analyzed.