Cooperative and Diminutive Effects of Pnicogen Bonds and Cation–π Interactions

The interplay between pnicogen bonds and cation–π interactions has been investigated at the MP2/aug‐cc‐pVDZ level. Interesting cooperative and diminutive effects are observed when pnicogen bonds and cation–π interactions coexist in the same complex. These effects have been analyzed in terms of the structural, energetic, and charge‐transfer properties of the complexes. The variations in electron density at critical points of the intermolecular bond have been used to analyze bond strengthening or weakening. The nature of the interactions and the mechanisms of cooperative and diminutive effects have been studied by means of symmetry‐adapted perturbation theory and molecular electrostatic potentials.     

Exergonic and Spontaneous Production of Radicals through Beryllium Bonds

High‐level ab initio calculations show that the formation of radicals, by the homolytic bond fission of Y?R (Y=F, OH, NH₂; R=CH₃, NH₂, OH, F, SiH₃, PH₂, SH, Cl, NO) bonds is dramatically favored by the association of the molecule with BeX₂ (X=H and Cl) derivatives. This finding is a consequence of two concomitant effects, the significant activation of the Y?R bond after the formation of the beryllium bond, and the huge stabilization of the F^. (OH^., NH₂^.) radical upon BeX₂ attachment. In those cases where R is an electronegative group, the formation of the radicals is not only exergonic, but spontaneous.     

Theoretical Study on Cooperativity Effects between Anion–π and Halogen‐Bonding Interactions

This article analyzes the interplay between lone pair–π (lp–π) or anion–π interactions and halogen‐bonding interactions. Interesting cooperativity effects are observed when lp/anion–π and halogen‐bonding interactions coexist in the same complex, and they are found even in systems in which the distance between the anion and halogen‐bond donor molecule is longer than 9 Å. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods. Bader′s theory of “atoms in molecules” is used to characterize the interactions and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The physical nature of the interactions and cooperativity effects are studied by means of molecular interaction potential with polarization partition scheme. By taking advantage of all aforementioned computational methods, the present study examines how these interactions mutually influence each other. Additionally, experimental evidence for such interactions is obtained from the Cambridge Structural Database (CSD).     

Creating σ‐Holes through the Formation of Beryllium Bonds

Through the use of ab initio theoretical models based on MP2/aug‐cc‐pVDZ‐optimized geometries and CCSD(T)/aug‐cc‐pVTZ and CCSD(T)/aug‐c‐pVDZ total energies, it has been shown that the significant electron density rearrangements that follow the formation of a beryllium bond may lead to the appearance of a σ‐hole in systems that previously do not exhibit this feature, such as CH₃OF, NO₂F, NO₃F, and other fluorine‐containing systems. The creation of the σ‐hole is another manifestation of the bond activation–reinforcement (BAR) rule. The appearance of a σ‐hole on the F atoms of CH₃OF is due to the enhancement of the electronegativity of the O atom that participates in the beryllium bond. This atom recovers part of the charge transferred to Be by polarizing the valence density of the F into the bonding region. An analysis of the electron density shows that indeed this bond becomes reinforced, but the F atom becomes more electron deficient with the appearance of the σ‐hole. Importantly, similar effects are also observed even when the atom participating in the beryllium bond is not directly attached to the F atom, as in NO₂F, NO₃F, or NCF. Hence, whereas the isolated CH₃OF, NO₂F, and NO₃F are unable to yield F ??? Base halogen bonds, their complexes with BeX₂ derivatives are able to yield such bonds. Significant cooperative effects between the new halogen bond and the beryllium bond reinforce the strength of both noncovalent interactions.     

DFT Studies of Ag‐Loading Intrinsic and Functionalized Single‐Walled Carbon Nanotubes

The first principles study was performed on the stability of Ag adsorbed on the internal walls of single‐walled carbon nanotube (SWCNT) and loaded on acid modified SWCNT. The calculation results show that Ag can be adsorbed stably on the internal walls of SWCNT. With the increase of SWCNT diameter, the adsorption energy increases in a certain range. Ag can also be loaded on the modified SWCNT surface in the form of COOAg and OAg groups, and COOAg group is more stable than OAg group. For either the adsorption on the inner SWCNT or the load on the modified SWCNT surface, only a small proportion of the Ag ions can be stably bonded to the walls of SWCNT.     

How Good is Fluorine as a Hydrogen‐Bond Acceptor in Fluorinated Single‐Walled Carbon Nanotubes?

Ab initio (RI-MP2/TZVPP) computations were employed to investigate the interaction between hydrogen-bond donors H2O and CH3OH and covalently bound fluorine in organofluorine compounds. While the CFHO interaction energy is around 3 kcal mol(-1) for unstrained systems, the linear correlation between pyramidalization angle at the carbon atom and the interaction energy suggests that increased binding can be obtained in strained systems. This is confirmed for the dihydrodifluoropyrene-methanol pair, but a large portion of the binding energy is due to the interaction of the pi system with the oxygen atom. Density functional periodic boundary condition computations (PBC-PBE/6-31G*) of the structures of (5,5) and (10,10) armchair (C2F)n fluorinated SWNTs (F-SWNTs) indicate that the pyramidalization at the fluorine-binding carbon atoms are too similar to that of CH3F to enhance the hydrogen-bond acceptor properties of fluorine significantly. The solubility of F-SWNTs in alcohols therefore could be due to a combination of hydrogen bonds and van der Waals interactions with the pi systems.     

Structural Preferences of Single‐Walled Silica Nanostructures: Nanospheres and Chemically Stable Nanotubes

Structural preferences of single‐walled and coordinatively saturated spherical and tubular nanostructures of silica have been determined by ab initio calculations. Two families of spherical (SiO₂)_n clusters derived from Platonic solids and Archimedean polyhedra are depicted, with n ranging from 4–120. The analogue of a truncated icosidodecahedron, I_h‐symmetric Si₁₂₀O₂₄₀, is favored in energy, closely followed by the I_h‐symmetric Si₆₀O₁₂₀‐truncated icosahedron. The silica nanotubes derived from spherical clusters are capped by Si₂O₂ rings, whereas the tubular section consists of single oxygen bridges. Periodic studies performed with open‐ended silica nanotubes and the α‐quartz polymorph of silica, along with a comparisons to fullerenes and carbon nanotubes, suggest that tubes with diameters of approximately 1 nm should be chemically stable.     

Competition between Intra and Intermolecular Pnicogen Bonds: Complexes between Naphthalene Derivatives and Neutral or Anionic Bases

The PnF₂ (Pn=P,As,Sb,Bi) on a naphthalene scaffold can engage in an internal pnicogen Pn⋅⋅⋅N bond (PnB) with an NH₂ group placed close to it on the adjoining ring. An approaching neutral NH₃ molecule can engage in a second PnB with the central Pn, which tends to weaken the intramolecular bond. The presence of the latter in turn weakens the intermolecular PnB with respect to that formed in its absence. Replacement of the external NH₃ by a CN⁻ anion causes a fundamental change in the bonding pattern, producing a fourth covalent bond with Pn, which rearranges into a trigonal bipyramidal motif. This addition disrupts the internal Pn⋅⋅⋅N pnicogen bond, recasting the PnF₂⋅⋅⋅NH₂ interaction into an NH⋅⋅⋅F H-bond.     

Enhanced Li Adsorption and Diffusion in Single‐Walled Silicon Nanotubes: An ab Initio Study

We report a first‐principles investigation of Li adsorption and diffusion in single‐walled Si nanotubes (SWSiNTs) of interest to Li‐ion battery anodes. We calculate Li insertion characteristics in SWSiNTs and compare them with the respective ones in carbon nanotubes (CNTs) and other silicon nanostructures. From our calculations, SWSiNTs show higher reactivity toward the adsorption of Li adatoms than CNTs and Si nanoclusters. Considering the importance of Li kinetics, we demonstrate that the interior of SWSiNTs may serve as a fast Li diffusion channel. The important advantage of SWSiNTs over their carbon analogues is a sevenfold reduction in the energy barrier for the penetration of the Li atoms into the nanotube interior through the sidewalls. This prepossesses easier Li diffusion inside the tube and subsequent utilization of the interior sites, which enhances Li storage capacity of the system. The improvements in both Li uptake and Li mobility over their analogues support the great potential of SWSiNTs as Li‐ion battery anodes.     

Ternary Complexes Stabilized by Chalcogen and Alkaline-Earth Bonds: Crucial Role of Cooperativity and Secondary Noncovalent Interactions

High-level G4 calculations show that the strength of chalcogen interactions is enhanced dramatically if chalcogen compounds simultaneously form alkaline-earth bonds. This phenomenon is studied by exploring binary YX₂⋅⋅⋅N-Base complexes and two types of ternary MCl₂⋅⋅⋅YX₂⋅⋅⋅N-Base, YX₂⋅⋅⋅N-Base⋅⋅⋅MCl₂ complexes, in which YX₂ is a chalcogen compound (Y=S, Se; X=F, Cl), the N-Bases are sp, sp², and sp³ bases (NCH, HN=CH₂, NH₃), and MCl₂ are alkaline-earth BeCl₂ or MgCl₂ derivatives. Starting from the chalcogen-bonded complexes YX₂⋅⋅⋅NH₃ and YX₂⋅⋅⋅HN=CH₂, the binding site of a new incoming alkaline-earth bond is found, surprisingly, to depend on the nature of the halogen atom attached to the chalcogen. For the YF₂ binary complexes the association site is the F atom of the YF₂ subunit, whereas for YCl₂ it is the N atom of the nitrogen base. Regarding YX₂⋅⋅⋅NCH complexes, N is the most favorable site for an alkaline-earth interaction in ternary complexes, regardless of which YX₂ derivative is used. The explanation relies on the interplay of all the noncovalent interactions involved: the strong cooperativity between chalcogen and alkaline-earth bonds, and the appearance of secondary noncovalent interactions in the form of hydrogen bonds.     

Theoretical Study on the Dual Behavior of XeO3 and XeF4 toward Aromatic Rings: Lone Pair–π versus Aerogen–π Interactions

In this study, several lone pair–π and aerogen–π complexes between XeO₃ and XeF₄ and aromatic rings with different electronic natures (benzene, trifluorobenzene, and hexafluorobenzene) are optimized at the RI‐MP2/aug‐cc‐pVTZ level of theory. All complexes are characterized as true minima by frequency analysis calculations. The donor/acceptor role of the ring in the complexes is analyzed using the natural bond orbital computational tool, showing a remarkable contribution of orbital interactions to the global stabilization of the aerogen–π complexes. Finally, Bader's AIM analysis of several complexes is performed to further characterize the lone pair–π and aerogen–π interactions.     

Very Long‐Range Effects: Cooperativity between Anion–π and Hydrogen‐Bonding Interactions

The interplay between two important non‐covalent interactions involving aromatic rings (namely anion–π and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion–π and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen‐bond donor/acceptor molecule is as long as ～11 Å. These effects are studied theoretically using the energetic and geometric features of the complexes, which were computed using ab initio calculations. We use and discuss several criteria to analyze the mutual influence of the non‐covalent interactions studied herein. In addition we use Bader’s theory of atoms‐in‐molecules to characterize the interactions and to analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.     

Host–Guest Chemistry: Oxoanion Recognition Based on Combined Charge‐Assisted C−H or Halogen‐Bonding Interactions and Anion⋅⋅⋅Anion Interactions Mediated by Hydrogen Bonds

Several bis‐triazolium‐based receptors have been synthesized and their anion‐recognition capabilities have been studied. The central chiral 1,1′‐bi‐2‐naphthol (BINOL) core features either two aryl or ferrocenyl end‐capped side arms with central halogen‐ or hydrogen‐bonding triazolium receptors. NMR spectroscopic data indicate the simultaneous occurrence of several charge‐assisted aliphatic and heteroaromatic C?H noncovalent interactions and combinations of C?H hydrogen and halogen bonding. The receptors are able to selectively interact with HP₂O₇^3?, H₂PO₄^?, and SO₄^2? anions, and the value of the association constant follows the sequence: HP₂O₇^3?>SO₄^2?>H₂PO₄^?. The ferrocenyl end‐capped 7²⁺?2 BF₄ ^? receptor allows recognition and differentiation of H₂PO₄^? and HP₂O₇^3? anions by using different channels: H₂PO₄^? is selectively detected through absorption and emission methods and HP₂O₇^3? by using electrochemical techniques. Significant structural results are the observation of an anion???anion interaction in the solid state (2:2 complex, 6²⁺? [ H₂P₂O₇ ] ^2? ), and a short C?I???O contact is observed in the structure of the complex [ 8 ²⁺][SO₄]_0.5[BF₄].     

Intermolecular Interactions in Weak Donor–Acceptor Complexes from Symmetry‐Adapted Perturbation and Coupled‐Cluster Theory: Tetracyanoethylene–Benzene and Tetracyanoethylene–p‐Xylene

The interactions in the complexes of tetracyanothylene (TCNE) with benzene and p‐xylene, often classified as weak electron donor–acceptor (EDA) complexes, are investigated by a range of quantum chemical methods including intermolecular perturbation theory at the DFT‐SAPT (symmetry‐adapted perturbation theory combined with density functional theory) level and explicitly correlated coupled‐cluster theory at the CCSD(T)‐F12 level. The DFT‐SAPT interaction energies for TCNE–benzene and TCNE–p‐xylene are estimated to be ?35.7 and ?44.9 kJ mol^?1, respectively, at the complete basis set limit. The best estimates for the CCSD(T) interaction energy are ?37.5 and ?46.0 kJ mol^?1, respectively. It is shown that the second‐order dispersion term provides the most important attractive contribution to the interaction energy, followed by the first‐order electrostatic term. The sum of second‐ and higher‐order induction and exchange–induction energies is found to provide nearly 40 % of the total interaction energy. After addition of vibrational, rigid‐rotor, and translational contributions, the computed internal energy changes on complex formation approach results from gas‐phase spectrophotometry at elevated temperatures within experimental uncertainties, while the corresponding entropy changes differ substantially.     

Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

Genomic DNA in bacteria exists in a condensed state, which exhibits different biochemical and biophysical properties from a dilute solution. DNA was concentrated on streptavidin‐covered single‐walled carbon nanotubes (Strep ? SWNTs) through biotin–streptavidin interactions. We reasoned that confining DNA within a defined space through mechanical constraints, rather than by manipulating buffer conditions, would more closely resemble physiological conditions. By ensuring a high streptavidin loading on SWNTs of about 1 streptavidin tetramer per 4 nm of SWNT, we were able to achieve dense DNA binding. DNA is bound to Strep ? SWNTs at a tunable density and up to as high as 0.5 mg mL^?1 in solution and 29 mg mL^?1 on a 2D surface. This platform allows us to observe the aggregation behavior of DNA at high concentrations and the counteracting effects of HU protein (a histone‐like protein from Escherichia coli strain U93) on the DNA aggregates. This provides an in vitro model for studying DNA–DNA and DNA–protein interactions at a high DNA concentration.     

Contributions of Various Noncovalent Bonds to the Interaction between an Amide and S‐Containing Molecules

N‐Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH₃SH, CH₃SCH₃, and CH₃SSCH₃ as models of S‐containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH???O, NH???S, CH???O, CH???S, SH???π, and CH???π H‐bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H‐bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the global minimum, charge‐transfer‐type noncovalent bonds play only a supporting role. The majority of dimers are bound by a collection of several of these attractive interactions. The SH???O and NH???S H‐bonds are of comparable strength, followed by CH???O and CH???S.