Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone

The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH₂ groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH₂. The trends in the energy decomposition analysis for the interaction energy, ΔE_int, showed that the ΔE_elstat contributions are equal or even a little bit higher than the values for ΔE_disp. Such important ΔE_elstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH₂ functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔE_disp is the most important attractive contribution to the ΔE_int. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.

CH-π Interactions in Glycan Recognition

Carbohydrate recognition is crucial for biological processes ranging from development to immune system function to host-pathogen interactions. The proteins that bind glycans are faced with a daunting task: to coax these hydrophilic species out of water and into a binding site. Here, we examine the forces underlying glycan recognition by proteins. Our previous bioinformatic study of glycan-binding sites indicated that the most overrepresented side chains are electron-rich aromatic residues, including tyrosine and tryptophan. These findings point to the importance of CH-π interactions for glycan binding. Studies of CH-π interactions show a strong dependence on the presence of an electron-rich π system, and the data indicate binding is enhanced by complementary electronic interactions between the electron-rich aromatic ring and the partial positive charge of the carbohydrate C-H protons. This electronic dependence means that carbohydrate residues with multiple aligned highly polarized C-H bonds, such as β-galactose, form strong CH-π interactions, whereas less polarized residues such as α-mannose do not. This information can guide the design of proteins to recognize sugars and the generation of ligands for proteins, small molecules, or catalysts that bind sugars.

Synthesis of Azacalixarenes and Development of Their Properties

This review focuses on the synthesis, structure, and interactions of metal ions, the detection of some weak interactions using the structure, and the construction of supramolecules of azacalixarenes that have been reported to date. Azacalixarenes are characterized by the presence of shallow or deep cavities, the simultaneous presence of a basic nitrogen atom and an acidic phenolic hydroxyl group, and the ability to introduce various side chains into the cyclic skeleton. These molecules can be given many functions by substituting groups on the benzene ring, modifying phenolic hydroxyl groups, and converting side chains. The author discusses the evidence of azacalixarene utilizing these characteristics.

A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs

This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.

Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry

Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.

The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates

The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.

CH/π Interactions in DNA and Proteins. A Theoretical Study

A systematic study of the CH/pi interactions of methane with the purine and pyrimidine bases of nucleic acids and with the lateral chains of the four natural aromatic amino acids has been carried out for the first time. The MPWB1K/6-31+G(d,p) method has shown to be adequate for the study of these weak interactions in which dispersion forces play a main role. It has been shown that two different kinds of clusters exist, depending on whether one or two CH bonds point to the aromatic system. The latter one, which we have called bifurcated, is usually more stable. With regard to aromatic amino acids, our calculations agree with experimental data in the fact that tryptophan leads to the strongest interaction, while hystidine leads to the weakest one. In the case of nucleic acid bases, the differences in binding energies are not large. This is specially true for thymine and uracil, showing that these two bases have a similar acceptor character in CH/pi interactions.

Multi-input–Multi-output Molecular Response System Based on Dynamic Redox Behavior of Hexaphenylethane-type Electron Donors with the Tetrahydrophenanthrazepine Skeleton: Strong Chiroptical Signals through the Transmission of Point Chirality to Helicity

The title heterocyclic donors undergo reversible C-C bond formation/cleavage upon electron transfer (dynamic redox behavior). The helical sense in both neutral and cationic states is interconvertible by facile ring flipping. The pi-type asymmetric center on the azepine nitrogen atom induces a significant degree of diasteromeric preference, thus endowing strong CD activity based on exciton coupling. Chiroptical properties could be modified not only by redox reactions but also by heat and protonation. The present redox pairs can serve as unprecedented three-way-input (e, H+, delta) and two-way-output (UV/Vis, CD) response systems.

Origin of the π-Facial Stereoselectivity in the Addition of Nucleophilic Reagents to Chiral Aliphatic Ketones as Evidenced by High-Level Ab Initio Molecular-Orbital Calculations

Ab initio molecular-orbital (MO) calculations were carried out, at the MP2/6-311++G(d,p)//MP2/6-31G(d) level, to investigate the conformational Gibbs energy of alkyl 1-cyclohexylethyl ketones, cyclo-C6H11CHCH3-CO-R (R = Me, Et, iPr, and tBu). In each case, one of the equatorial conformations was shown to be the most stable. Conformers with the axial CHCH3COR group were also shown to be present in an appreciable concentration. Short C-H...C=O and C-H...O=C distances were found in each stable conformation. The result was interpreted on the grounds of C-H...pi(C=O) and C-H...O hydrogen bonds, which stabilize the geometry of the molecule. The ratio of the diastereomeric secondary alcohols produced in the nucleophilic addition to cyclo-C6H11CHCH3-CO-R was estimated on the basis of the conformer distribution. The calculated result was consistent with the experimental data previously reported: the gradual increase in the product ratio (major/minor) along the series was followed by a drop at R = tBu. The energy of the diastereomeric transition states in the addition of LiH to cyclo-C6H11CHCH3-CO-R was also calculated for R = Me and tBu. The product ratio did not differ significantly in going from R = Me to tBu in the case of the aliphatic ketones. This is compatible with the above result calculated on the basis of the conformer distribution. Thus, the mechanism of the pi-facial selection can be explained in terms of the simple premise that the geometry of the transition state resembles the ground-state conformation of the substrates and that the nucleophilic reagent approaches from the less-hindered side of the carbonyl pi face.

Magnitude and Directionality of the Interaction Energy of the Aliphatic CH/π Interaction: Significant Difference from Hydrogen Bond

The CCSD(T) level interaction energies of CH/pi complexes at the basis set limit were estimated. The estimated interaction energies of the benzene complexes with CH(4), CH(3)CH(3), CH(2)CH(2), CHCH, CH(3)NH(2), CH(3)OH, CH(3)OCH(3), CH(3)F, CH(3)Cl, CH(3)ClNH(2), CH(3)ClOH, CH(2)Cl(2), CH(2)FCl, CH(2)F(2), CHCl(3), and CH(3)F(3) are -1.45, -1.82, -2.06, -2.83, -1.94, -1.98, -2.06, -2.31, -2.99, -3.57, -3.71, -4.54, -3.88, -3.22, -5.64, and -4.18 kcal/mol, respectively. Dispersion is the major source of attraction, even if substituents are attached to the carbon atom of the C-H bond. The dispersion interaction between benzene and chlorine atoms, which is not the CH/pi interaction, is the cause of the very large interaction energy of the CHCl(3) complex. Activated CH/pi interaction (acetylene and substituted methanes with two or three electron-withdrawing groups) is not very weak. The nature of the activated CH/pi interaction may be similar to the hydrogen bond. On the other hand, the nature of other typical (nonactivated) CH/pi interactions is completely different from that of the hydrogen bond. The typical CH/pi interaction is significantly weaker than the hydrogen bond. Dispersion interaction is mainly responsible for the attraction in the CH/pi interaction, whereas electrostatic interaction is the major source of attraction in the hydrogen bond. The orientation dependence of the interaction energy of the typical CH/pi interaction energy is very small, whereas the hydrogen bond has strong directionality. The weak directionality suggests that the hydrogen atom of the interacting C-H bond is not essential for the attraction and that the typical CH/pi interaction does not play critical roles in determining the molecular orientation in molecular assemblies.

Magnitude of the CH/π Interaction in the Gas Phase: Experimental and Theoretical Determination of the Accurate Interaction Energy in Benzene-methane

The accurate CH/pi interaction energy of the benzene-methane model system was experimentally and theoretically determined. In the experiment, mass analyzed threshold ionization spectroscopy was applied to the benzene-methane cluster in the gas phase, prepared in a supersonic molecular beam. The binding energy in the neutral ground state of the cluster, which is regarded as the CH/pi interaction energy for this model system, was evaluated from the dissociation threshold measurements of the cluster cation. The experimentally determined binding energy (D(0)) was 1.03-1.13 kcal/mol. The interaction energy of the model system was calculated by ab initio molecular orbital methods. The estimated CCSD(T) interaction energy at the basis set limit (D(e)) was -1.43 kcal/mol. The calculated binding energy (D(0)) after the vibrational zero-point energy correction (1.13 kcal/mol) agrees well with the experimental value. The effects of basis set and electron correlation correction procedure on the calculated CH/pi interaction energy were evaluated. Accuracy of the calculated interaction energies by DFT methods using BLYP, B3LYP, PW91 and PBE functionals was also discussed.

Polymorphism in Fe[(p-IC6H4)B(3-Mepz)3]2 (pz = Pyrazolyl): Impact of Supramolecular Structure on an Iron(II) Electronic Spin-State Crossover

The new ligands Na[(p-IC6H4)B(3-Rpz)3] (R = H, Me) have been prepared by converting I2C6H4 to IC6H4SiMe3 with Li(t)Bu and SiMe3Cl, and then to IC6H4BBr2 with BBr3 and subsequent reaction with 3 equiv of (un)substituted pyrazole and 1 equiv of NaO(t)Bu. These new ligands react with FeBr2 to give either purple, low-spin Fe[(p-IC6H4)B(pz)3]2 or colorless, high-spin Fe[(p-IC6H4)B(3-Mepz)3]2. Depending upon the crystallization conditions, Fe[(p-IC6H4)B(3-Mepz)3]2 can exist both as two polymorphs and as a methylene chloride solvate. An examination of these polymorphs by variable-temperature X-ray crystallography, magnetic susceptibility, and Mossbauer spectroscopy has revealed different electronic spin-state crossover properties for each polymorph and yields insight into the influence of crystal packing, independent of other electronic perturbations, on the spin-state crossover. The first polymorph of Fe[(p-IC6H4)B(3-Mepz)3]2 has a highly organized three-dimensional supramolecular structure and does not undergo a spin-state crossover upon cooling to 4 K. The second polymorph of Fe[(p-IC6H4)B(3-Mepz)3]2 has a stacked two-dimensional supramolecular structure, a structure that is clearly less well organized than that of the first polymorph, and undergoes an abrupt iron(II) spin-state crossover from high spin to low spin upon cooling below ca. 130 K. The crystal structure of the methylene chloride solvate of Fe[(p-IC6H4)B(3-Mepz)3]2 has a similar stacked two-dimensional supramolecular structure, but the crystals readily lose the solvate. The resulting desolvate undergoes a gradual spin-state crossover to the low-spin state upon cooling below ca. 235 K. It is clear from a comparison of the structures that the long-range solid-state organization of the molecules, which is controlled by noncovalent supramolecular interactions, has a strong impact upon the spin-state crossover, with the more highly organized structures having lower spin-crossover temperatures and more abrupt spin-crossover behavior.

CH/π hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase

The crystal structure of acetylcholine esterase (AchE) in complex with various inhibitors, investigated as drugs for improvement of the cognitive ability of early stage Alzheimer's disease, has been analyzed with the use of our program CHPI. A number of CH/pi hydrogen bonds have been disclosed in the binding of the inhibitors with Torpedo californica AchE. It has been demonstrated that, in order to be effective in the binding with AchE, C-H bonds in the inhibitor need not be polarized.