A theoretical study of substitution effects on halogen–π interactions

Recent advances in the strategic incorporation of fluorine into new-generation taxoid anticancer agents

This account describes our recent progress on the strategic incorporation of fluorine and organofluorine moieties into new-generation taxoid anticancer agents for medicinal chemistry and chemical biology studies. In the case study 1, novel 3rd-generation fluorotaxoids bearing 3-OCF3 or 3-OCF2H group in the C2-benzoate moiety were designed, synthesized and examined for their anticancer activities. The potency of novel taxoids against drug-resistant cancer cell lines was 2-3 orders of magnitude higher than that of paclitaxel (PTX). Molecular modeling analysis indicated the favorable van der Waals interactions of OCF3 and OCHF2 groups in the binding site. Overall, taxoids bearing a OCHF2 group at the C2 benzoate position exhibited the highest potencies against multidrug-resistant (MDR) cancer cell lines and cancer stem cell (CSC)-enriched cell lines, indicating that the new 3rd-generation fluorotaxoids are promising candidates as chemotherapeutic agents. In the case study 2, novel 3rd-generation 3'-difluorovinyl (DFV)-taxoids, bearing 3-CF3O or 3-CHF2O group in the C2-benzoyl moiety, were designed, synthesized, and evaluated for their potencies and pharmacological properties. These new DFV-taxoids exhibited remarkable cytotoxicity against extremely drug-resistant cancer cell lines with subnanomolar IC50 values, indicating that these new DFV-taxoids can overcome MDR caused by the overexpression of Pgp and other ABC cassette transporters. The molecular docking analysis of new DFV-taxoids revealed that the 3'-DFV moiety and the 3-CF3O/3-CHF2O group of the C2-benzoate moiety are nicely accommodated to the deep hydrophobic pocket of the PTX/taxoid binding site in the β-tubulin, enabling an enhanced binding through unique attractive interactions between F/OCF3/OCHF2 and the protein. This enhancement in binding is reflected in the remarkable high potency of new 3rd-generation DFV-taxoids. In the case study 3.1, the therapeutic potential of new 3rd-generation DFV-taxoids in anaplastic thyroid cancer (ATC) cells was evaluated in vitro and in vivo. This study demonstrated that these new DFV-taxoids were more efficacious than PTX against ATC cell lines and tumor xenografts, as demonstrated by the efficient inhibition of cell proliferation and colony formation, induction of apoptosis via the mitotic arrest at the G2/M phase, as well as the suppression of tumorigenic potential in nude mice. Furthermore, tubulin polymerization assay and molecular docking analysis confirmed that these new DFV-taxoids promoted far more rapid polymerization of β-tubulin than PTX through stronger binding to tubulin/microtubules. Taken together, this study has indicated a promising therapeutic potential of these new DFV-taxoids against ATC. In the case study 3.2, DFV-OTX displayed potent cytotoxicity and effective induction of β-tubulin polymerization, as well as the G2/M phase arrest, leading to apoptosis in PTX-sensitive and PTX-resistant breast cancer cells. Furthermore, DFV-OTX clearly exhibited efficacy against MCF-7R and MDA-MB-231R tumor xenografts in mouse models. Thus, DFV-OTX effectively overcame PTX-resistance in MDA-MB-231R cells and tumor xenografts, wherein the drug resistance was attributed to ABCB1/ABCG2 upregulation. DFV-OTX was also effective against MCF-7R cells and tumor xenografts, which are PTX-resistant due to different MOA. Accordingly, DFV-OTX is a promising chemotherapeutic agent for the treatment of PTX-resistant cancers. Overall, these next-generation fluorotaxoids are promising candidates for highly potent chemotherapeutic agents, as well as payloads for tumor-targeting drug conjugates such as antibody-drug conjugates (ADCs).

Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction

Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Nature of halogen bonding involving π-systems, nitroxide radicals and carbenes: a highlight of the importance of charge transfer

The recently developed adiabatic absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) has proven to be useful in determining the effects of different energy components on the geometries of complexes bound by intermolecular interactions. The authors have applied it to systems such as the water dimer, water-ion complexes, metallocenes and lone-pair type halogen-bonded (XB) dimers. In this study, we have extended the second-generation ALMO-EDA method to 40 different XB complexes by benchmarking against its classical counterpart and symmetry-adapted perturbation theory (SAPT). In addition, we have examined the nature of halogen bonding involving less studied XB acceptors, namely π-systems, radicals and carbenes, using the adiabatic ALMO-EDA analyses, particularly to shed light on how each energy component affects the geometries of the XB complexes. Our results show that the second-generation ALMO-EDA predicts a higher electrostatic energy contribution in all XB complexes compared to SAPT and classical ALMO-EDA schemes. On the other hand, when comparing across different XB acceptors, all three partition schemes produced the same qualitative finding. The adiabatic ALMO-EDA analyses indicate that while the inclusion of a charge transfer contribution is important in achieving accurate XB bond lengths and interaction energies, as well as recovering the binding site specificity of XB involving benzene and naphthalene acceptors, it is sufficient to obtain the linearity of the XB complexes in the frozen approximation.

Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F)

Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.

Cooperative and substitution effects in enhancing the strength of fluorine bonds by anion−π interactions

In this work, the cooperative effects between anion−π and fluorine bond interactions are studied by ab initio calculations at the MP2/6-311++G** level. Cooperative effects are observed in complexes in which anion−π and fluorine bond interactions coexist. For each complex, the shortening of the binding distance in the fluorine bond is more prominent than that in the anion−π bond. Favorable cooperativity energies are found with values that range between –0.51 and –0.76 kcal/mol. The atoms in molecules and molecular electrostatic potential analyses are carried out for these complexes to understand the nature of anion−π and fluorine bond interactions and the origin of the cooperativity.

An ab initio study on tunability of σ-hole interactions in XHS:PH2Y and XH2P:SHY complexes (X = F, Cl, Br; Y = H, OH, OCH3, CH3, C2H5, and NH2)

Quantum chemical calculations are performed to investigate the tunability of σ-hole interactions in chalcogen-bonded XHS:PH2Y and pnicogen-bonded XH2P:SHY complexes, where X  =  F, Cl, Br and Y  =  H, OH, OCH3, CH3, C2H5, NH2. The formation of these binary complexes can be understood in terms of molecular electrostatic potentials (MEPs), considering the P and S atoms as an electron acceptor or an electron donor in the chalcogen and pnicogen bonds. The strength of the XHS:PH2Y and XH2P:SHY complexes for a given Y increases as follows: X = Br < Cl < F. In addition, an acceptable linear relationship is found between the interaction energies and the magnitudes of the product of most positive and negative MEPs. This finding along with the electron density difference maps provides a clear picture of the electrostatic nature of the interactions in the XHS:PH2Y and XH2P:SHY complexes. The calculated spin-spin coupling constants across the chalcogen bond interactions in the XHS:PH2Y complexes display a quadratic dependence with the P···S binding distance.

On the properties of S⋯O and S⋯π noncovalent interactions: the analysis of geometry, interaction energy and electron density

We report computational studies on the origin and magnitude of non-covalent S⋯O and S⋯π interactions.

CNXeCl and CNXeBr species as halogen bond donors: a quantum chemical study on the structure, properties, and nature of halogen···nitrogen interactions

In the present study, strength and characteristic of halogen bond interactions between CNXeY and NCZ molecules are investigated, where Y = Cl, Br and Z = H, CN, F, OH, CH₃, OCH₃, NH₂. MP2/aug-cc-pVTZ calculations indicate that the interaction energies for CNXeY⋯NCZ complexes lie in the range between -1.0 and -3.1 kcal mol⁻¹. Not surprisingly, the calculated interaction energies show a strong correlation with the negative electrostatic potentials on nitrogen atoms. One of the most important results of this study is that, according to energy decomposition analyses, Cl⋯N halogen bonds are largely dependent on dispersion effects, while electrostatic interactions are the major source of the attraction in Br⋯N bonds. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis are used in this study to deepen the nature of the interactions considered. This appears to be the first report on a halogen bond involving halogenated xenon isocyanides.