Computational Study about Through-Bond and Through-Space Interactions in [2.2]Cyclophanes

Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes

Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = H2O, NH3, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < H2O < MeOH < NH3. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.

Strained thiacyclophanes: Reducing properties and gauge of transannular interactions

The current study involves the investigation of reducing properties of disulfide bonded heteraphanes. The calculated adiabatic electron affinity (AEA) values of heteraphanes are found comparable to that of cystine molecule and are capable of undergoing reversible redox reactions. In aqueous phase, these show high propensity to get reduced. The reaction energies calculated using isodesmic equations reflect the strain associated with the studied thiacyclophane models. Increase in the number of disulfide bonds results in less strain and more stabilization. Through-space transannular interactions in the selected heteraphanes have a decisive influence on the structure stabilization associated with the systems. The results reported in the current study are expected to play a vital role while designing redox driven drug carriers by incorporating these systems in biomolecules.

Bader's Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction-Proof Studies Based on the Ng@[3n]cyclophane Endohedral Complexes

According to Bader's quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly 'troublesome' are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host's cage system usually 'produces' many counterintuitive bond paths. In the author's opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host's cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3n]cyclophane (3≤n≤6) endohedral complexes is used. As a result, arguments are presented showing that Bader's topological bond path does not necessarily indicate a stabilizing interaction.

Toward functionalization of ZnO nanotubes and monolayers with 5-aminolevulinic acid drugs as possible nanocarriers for drug delivery: a DFT based molecular dynamic simulation

We have investigated the interactions between a 5-aminolevulinic acid (ALA) drug and ZnO nanostructures including ZnO monolayers and ZnO nanotubes (ZnONTs) using density functional theory (DFT) calculations. In the context of the dispersion corrected Perdew-Burke-Ernzerhof (PBE) approach, the energetics, charge transfer, electronic structure and equilibrium geometries have been estimated. As ALA is adsorbed onto/into the ZnONTs and on the ZnO monolayer with interaction energies (Eint) of -2.55/-2.75 eV and -2.51 eV, respectively, the calculated Eint values and bonding distances (∼2 Å) reveal that the interaction type is chemisorption. The ZnO nanostructures showed promising performance in the ALA drug functionalization, taking into account the interaction energy values. The band gap almost remains unchanged for both of the substrates under consideration after ALA adsorption, and the semiconductor properties of the substrates are preserved, according to the analyzed density of states (DOSs) spectra. The interaction nature of the ALA-ZnO nanostructures according to the atom in molecule (AIM) analysis was found to be polar attraction with partial covalent bonding between O and Zn. Our DFT based molecular dynamic (MD) simulation results demonstrate that, in the aqueous solution, ALA moves toward the interior sidewall of the ZnONTs and ZnO nanosheet surface and binds to the Zn atom through its O (carbonyl/hydroxyl groups) and N atoms and the hydroxyl H atom was dissociated and binds to the O atom of the ZnO surface. However, in the case of ALA adsorption onto the outer surface of ZnONTs, only the O atoms of carbonyl groups bind to the Zn atom and the structure of the drug remains undestroyed during the adsorption. The current findings shed light on the polar drug adsorption/encapsulation behavior on/into ZnO nanostructures, which may encourage further use of ZnO-based nanomaterials in the field of drug delivery and bio-functionalized nanomaterials.

Determining Repulsion in Cyclophane Cages

Superphane, i.e., [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane, is a very convenient molecule in studying the nature of guest⋯host interactions in endohedral complexes. Nevertheless, the presence of as many as six ethylene bridges in the superphane molecule makes it practically impossible for the trapped entity to escape out of the superphane cage. Thus, in this article, I have implemented the idea of using the superphane derivatives with a reduced number of ethylene linkers, which leads to the [2n] cyclophanes where n<6. Seven such cyclophanes are then allowed to form endohedral complexes with noble gas (Ng) atoms (He, Ne, Ar, Kr). It is shown that in the vast majority of cases, the initially trapped Ng atom spontaneously escapes from the cyclophane cage, creating an exohedral complex. This is the best proof that the Ng⋯cyclophane interaction in endohedral complexes is indeed highly repulsive, i.e., destabilizing. Apart from the ‘sealed’ superphane molecule, endohedral complexes are only formed in the case of the smallest He atom. However, it has been shown that in these cases, the Ng⋯cyclophane interaction inside the cyclophane cage is nonbonding, i.e., repulsive. This highly energetically unfavorable effect causes the cyclophane molecule to ‘swell’.

Endo- and exohedral complexes of superphane with cations

Quite recently it has been shown in a previous study that superphane, that is, [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane, is a very convenient molecule in the study of endohedral complexes and especially in the study of the influence of the caged entity (i.e., guest) on the structure of the host molecule. This advantage results from the presence of two parallel benzene rings joined together by six quite flexible ethylene bridges (spacers). This article examines the energetic and structural properties of endo- and exohedral complexes of superphane with the following cations: H⁺ , Li⁺ , Na⁺ , K⁺ , Be²⁺ , Mg²⁺ , Ca²⁺ , B³⁺ , Al³⁺ , Ga³⁺ . The stability of endohedral complexes has been shown to be strongly dependent on the charge and radius of the caged cation. The inclusion of the cation inside the superphane molecule causes its 'swelling', which is manifested by an increase in the distance between the benzene rings and elongations of the ring and spacer C-C bonds. In the case of exohedral complexes, three forms are investigated: with the cation above the benzene ring, with the cation interacting with the superphane window in the equatorial position, and with the cation interacting with the center of the C-C spacer bond. The first of these forms has been shown to be preferred. The cation⋯acceptor distance depends on the cation radius. Among the cations investigated, H⁺ and Be²⁺ are particularly reactive and predisposed to induce significant structural changes in the superphane molecule, forming C-H bond or C-Be-C bridges, respectively.

Thiourea Organocatalysts as Emerging Chiral Pollutants: En Route to Porphyrin-Based (Chir)Optical Sensing

Environmental pollution with chiral organic compounds is an emerging problem requiring innovative sensing methods. Amino-functionalized thioureas, such as 2-(dimethylamino)cyclohexyl-(3,5-bis(trifluoromethyl)phenyl)thiourea (Takemoto’s catalyst), are widely used organocatalysts with virtually unknown environmental safety data. Ecotoxicity studies based on the Vibrio fischeri luminescence inhibition test reveal significant toxicity of Takemoto’s catalyst (EC50 = 7.9 mg/L) and its NH2-substituted analog (EC50 = 7.2–7.4 mg/L). The observed toxic effect was pronounced by the influence of the trifluoromethyl moiety. En route to the porphyrin-based chemosensing of Takemoto-type thioureas, their supramolecular binding to a series of zinc porphyrins was studied with UV-Vis and circular dichroism (CD) spectroscopy, computational analysis and single crystal X-ray diffraction. The association constant values generally increased with the increasing electron-withdrawing properties of the porphyrins and electron-donating ability of the thioureas, a result of the predominant Zn⋯N cation–dipole (Lewis acid–base) interaction. The binding event induced a CD signal in the Soret band region of the porphyrin hosts—a crucial property for chirality sensing of Takemoto-type thioureas.

The inspiration and challenge for through-space charge transfer architecture: from thermally activated delayed fluorescence to non-linear optical properties

Organic molecules consisting of electron donor (D) and electron acceptor (A) subunits linked by π-conjugated bridges are promising building blocks for thermally activated delayed fluorescence (TADF) and non-linear optics (NLO) materials due to their intramolecular charge transfer (CT) processes in response to external stimuli. According to the electron interaction pattern, the CT process in D-π-A architectures can be divided into two categories, through-bond/-space charge transfer (TB/TSCT). To date, research into the TADF properties of TSCT characteristic molecules has since seen significant growth. In fact, TSCT characteristic materials show great advantages in such NLO responses. In this perspective, we first briefly introduced the basic principles of NLO and TADF effects. Successively, we discuss the influence of TBCT and TSCT patterns on NLO and TADF properties, especially for TSCT characteristic. In the final part, we address the diversity and potential advantages of TSCT characteristic molecules as high-performance NLO materials. With these, it is expected that the greater structural flexibility of spatial conjugation can bring more functionality to NLO materials in the future.

What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?

Classical cyclophanes with two benzene rings have been compared with cyclophanes with one benzene ring replaced with an aliphatic part and aliphatic compounds, which are cyclophane analogues. Analysis of geometry, atomic charges, and aromatic and steric energy and investigation of intramolecular noncovalent interactions and charge mobility show that there is no special feature that distinguishes the classical cyclophanes from aliphatic analogues, so the definition of cyclophanes can be extended to other compounds.

Interplay between σ Holes, Anion···H-C, and Cation-π Interactions in Dibromo[2,2]paracyclophane Complexes

Theoretical calculations were performed to investigate the interplay between σ-hole, anion-HC and cation-π interactions in the complexes of dibromo[2,2]paracyclophane (DBr[2,2]PCP) with alkali (Li⁺, Na⁺, K⁺), alkaline earth metal cations (Be²⁺, Mg²⁺, and Ca²⁺), and halogen anions (F^-, Cl^-, and Br^-) using the wave function (MP2) and density functional theory (M06-2X and B3LYP) methods with the 6-311++G(d,p) basis set. The study reveals that DBr[2,2]PCP behaves as amphoteric molecule with a predominance of basic character. It prefers to interact with hard cations and hard anions such as Be²⁺ and F^- through cation-π and anion···HC interactions, respectively. Substitution of Br by F and Cl atoms in DBr[2,2]PCP decreases slightly the interaction energies of DX[2,2]PCP-halogen complexes (X = F, Cl, and Br) by 2.0 and 0.3 kcal/mol (M06-2X), respectively. The anion-HC interactions in DBr[2,2]PCP complexes are ∼10 kcal/mol stronger (B3LYP; ∼15 kcal/mol at M06-2X and 7 kcal/mol at MP2) than the σ-hole interactions.

Substituent effect on inter-ring interaction in paracyclophanes

The theoretical calculations, namely multipole-derived charge analysis, quantum theory of atom in molecules, and non-bonding interaction (NCI), were performed for [2.2]paracyclophanes, [2.2]paracyclophane-7,9-dienes, and [3.3]paracyclophanes optimized at B3LYP/6-311++G** level, including dispersion correction. The substituent effect of the electron donor N(Me)2 and electron acceptor NO2 group and the influence of the length of bridges joining the aromatic ring on aromatic ring interaction energy (AIE) and strain energy were discussed. The local and electrostatic character of the substituent effect in paracyclophanes was shown. The presence of the weak orbital through-space C···C interaction between the [3.3]paracyclophane ring and weak CH···O hydrogen bonds between the substituents in the different rings was shown.

in/out Isomerism of cyclophanes: a theoretical account of 2,6,15-trithia-[34,10][7]metacyclophane and [34,10][7]metacyclophane as well as their halogen substituted analogues

What are the effects responsible for cyclophane isomer stability?

Aromaticity and Through-Space Interaction between Aromatic Rings in [2.2]Paracyclophanes

The HOMA index calculated for [2.2]paracyclophanes in the solid state reveals a slight decrease of aromaticity. Interactions between aromatic rings of [2.2]paracyclophane have been investigated using AIM and NCI analysis in both crystal and optimized [2.2]paracyclophane structures. AIM analysis showed that the C···C bond path between the two aromatic rings is present only in few [2.2]paracyclophanes. The NCI approach visualized the dispersion and repulsive interactions between the aromatic rings of every [2.2]paracyclophane. Combination of AIM and the NCI approach is necessary for determining and identifying nonbonded interactions in [2.2]paracyclophanes.

Tuning the Electronic Coupling and Electron Transfer in Mo2 Donor-Acceptor Systems by Variation of the Bridge Conformation

Assembling two quadruply bonded dimolybdenum units [Mo2 (DAniF)3 ](+) (DAniF=N,N'-di(p-anisyl)formamidinate) with 1,4-naphthalenedicarboxylate and its thiolated derivatives produced three complexes [{Mo2 (DAniF)3 }2 (μ-1,4-O2 CC10 H6 CO2 )], [{Mo2 (DAniF)3 }2 (μ-1,4-OSCC10 H6 COS)], and [{Mo2 (DAniF)3 }2 (μ-1,4-S2 CC10 H6 CS2 )]. In the X-ray structures, the naphthalene bridge deviates from the plane defined by the two Mo-Mo bond vectors with the torsion angle increasing as the chelating atoms of the bridging ligand vary from O to S. The mixed-valent species exhibit intervalence transition absorption bands with high energy and very low intensity. In comparison with the data for the phenylene analogues, the optically determined electronic coupling matrix elements (Hab =258-345 cm(-1) ) are lowered by a factor of two or more, and the electron-transfer rate constants (ket ≈10(11)  s(-1) ) are reduced by about one order of magnitude. These results show that, when the electron-transporting ability of the bridge and electron-donating (electron-accepting) ability of the donor (acceptor) are both variable, the former plays a dominant role in controlling the intramolecular electron transfer. DFT calculations revealed that increasing the torsion angle enlarges the HOMO-LUMO energy gap by elevating the (bridging) ligand-based LUMO energy. Therefore, our experimental results and theoretical analyses verify the superexchange mechanism for electronic coupling and electron transfer.

Charge density investigations on [2,2]-paracyclophane – in data we trust

Four datasets on [2,2]-paracyclophane were collected in-house and at the Advanced Photon Source at two different temperatures for charge density investigation. Global data quality indicators such as high resolution, high I/σ(I) values, low merging R values and high multiplicity were matched for all four datasets. The structural parameters did not show significant differences, but the synchrotron data depicted deficiencies in the topological analysis. In retrospect these deficiencies could be assigned to the low quality of the innermost data, which could have been identified by e.g. merging R values for only these reflections. In the multipole refinement these deficiencies could be monitored using DRK-plot and residual density analysis. In this particular example the differences in the topological parameters were relatively small but significant.

[2.2.2]Paracyclophane, preference for η6 or η18 coordination mode including Ag(i) and Sn(ii): a survey into the cation–π interaction nature through relativistic DFT calculations

[2.2.2]Paracyclophane is a versatile π-cryptating structure, which can exhibit η²:η²:η² and η⁶:η⁶:η⁶ coordination with metal ions, involving two or six carbon atoms in each aromatic ring.

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.

Structure and NMR spectra of some [2.2]paracyclophanes. The dilemma of [2.2]paracyclophane symmetry

Density functional theory (DFT) quantum chemical calculations of the structure and NMR parameters for highly strained hydrocarbon [2.2]paracyclophane 1 and its three derivatives are presented. The calculated NMR parameters are compared with the experimental ones. By least-squares fitting of the (1)H spectra, almost all J(HH) coupling constants could be obtained with high accuracy. Theoretical vicinal J(HH) couplings in the aliphatic bridges, calculated using different basis sets (6-311G(d,p), and Huz-IV) reproduce the experimental values with essentially the same root-mean-square (rms) error of about 1.3 Hz, regardless of the basis set used. These discrepancies could be in part due to a considerable impact of rovibrational effects on the observed J(HH) couplings, since the latter show a measurable dependence on temperature. Because of the lasting literature controversies concerning the symmetry of parent compound 1, D(2h) versus D(2), a critical analysis of the relevant literature data is carried out. The symmetry issue is prone to confusion because, according to some literature claims, the two hypothetical enantiomeric D(2) structures of 1 could be separated by a very low energy barrier that would explain the occurrence of rovibrational effects on the observed vicinal J(HH) couplings. However, the D(2h) symmetry of 1 with a flat energy minimum could also account for these effects.

DFT study of [2.2]-, [3.3]-, and [4.4]paracyclophanes: strain energy, conformations, and rotational barriers

The three smallest symmetrical paracyclophanes, having tethers with two, three, or four methylene groups, have been examined with four density functional methods (B3LYP, M06-2x, B97-D, ωB97X-D). The geometries predicted by functionals accounting for medium-range correlation or long-range exchange and/or dispersion are in close agreement with experiment. In addition, these methods provide similar estimates of the strain energy of the paracylcophanes, which decrease with increasing tether length. [4.4]Paracyclophane is nearly strain-free, reflecting the small out-of-plane distortion of its phenyl rings. Lastly, the barrier for interconversion of the conformers of [3.3]paracylcophane is computed in close agreement with experiment, and an estimate for phenyl rotation in [4.4]paracyclophane of about 19 kcal mol(-1) is predicted by the DFT methods employed.