A Ditopic Ion-Pair Receptor Based on Stacked Nucleobase Quartets

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Probing the Lewis Acidity of Boronic Acids through Interactions with Arene Substituents

Boronic acids are Lewis acids that exist in equilibrium with boronate forms in aqueous solution. Here we experimentally and computationally investigated the Lewis acidity of 2,6‐diarylphenylboronic acids; specially designed phenylboronic acids that possess two flanking aromatic rings with tunable aromatic character. Hammett analysis of 2,6‐diarylphenylboronic acids reveals that their Lewis acidity remains unchanged upon the introduction of EWG/EDG at the distant para position of the flanking aromatic rings. Structural and computational studies demonstrate that polar‐π interactions and solvation effects contribute to the stabilization of boronic acids and boronate forms by aromatic rings. Our physical‐organic chemistry work highlights that boronic acids and boronates can be stabilized by aromatic systems, leading to an important molecular knowledge for rational design and development of boronic acid‐based catalysts and inhibitors of biomedically important proteins.

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺), and (post‐)transition metal (Zn²⁺, Cd²⁺, Hg²⁺, and Pb²⁺) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K⁺). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.

Do Sulfonamides Interact with Aromatic Rings?

Aromatic rings form energetically favorable interactions with many polar groups in chemical and biological systems. Recent molecular studies have shown that sulfonamides can chelate metal ions and form hydrogen bonds, however, it is presently not established whether the polar sulfonamide functionality also interacts with aromatic rings. Here, synthetic, spectroscopic, structural, and quantum chemical analyses on 2,6-diarylbenzenesulfonamides are reported, in which two flanking aromatic rings are positioned close to the central sulfonamide moiety. Fine-tuning the aromatic character by substituents on the flanking rings leads to linear trends in acidity and proton affinity of sulfonamides. This physical-organic chemistry study demonstrates that aromatic rings have a capacity to stabilize sulfonamides via through-space NH-π interactions. These results have implications in rational drug design targeting electron-rich aromatic rings in proteins.

Through-Space Polar-π Interactions in 2,6-Diarylthiophenols

Molecular recognition between polar groups and aromatic molecules is fundamentally important to rational drug design. Although it has been well established that many polar functionalities interact with electron-rich aromatic residues through energetically favorable polar-π interactions, there is a limited understanding of the association between thiols and aromatic systems. Herein we report physical-organic chemistry studies on 2,6-diarylthiophenols that possess the central thiophenol ring and two flanking aromatic rings with tunable electronic properties caused by substituents at distant para position. Hammett analysis revealed that pK_a values and proton affinities correlate well with Hammett sigma values of substituents. Additional energy decomposition analysis supported the conclusion that both through-space SH-π interactions and S^- -π interactions contribute to intramolecular stabilization of 2,6-diarylthiophenols.

Designing Self-Assembled Rosettes: Why Ammeline is a Superior Building Block to Melamine

In supramolecular chemistry, the rational design of self-assembled systems remains a challenge. Herein, hydrogen-bonded rosettes of melamine and ammeline have been theoretically examined by using dispersion-corrected density functional theory (DFT-D). Our bonding analyses, based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA), show that ammeline is a much better building block than melamine for the fabrication of cyclic complexes based on hydrogen bonds. This superior capacity is explained by both stronger hydrogen bonding and the occurrence of a strong synergy.

RNA versus DNA G-Quadruplex: The Origin of Increased Stability

DNA quadruplexes have been the subject of investigation because of their biological relevance and because of their potential application in supramolecular chemistry. Similarly, RNA quadruplexes are now gaining increasing attention. Although DNA and RNA quadruplexes are structurally very similar, the latter show higher stability. In this study we report dispersion‐corrected density functional theory (DFT‐D) quantum chemical calculations that were undertaken to understand the difference in stabilities of RNA and DNA quadruplexes. The smallest meaningful model of a stack of quartets, interacting with alkali metal cations, was simulated in an aqueous environment. The energy decomposition analysis allows for in‐depth examination of the interaction energies, emphasising the role of noncovalent interactions and better electrostatics in determining RNA‐GQs higher stabilities, particularly pinpointing the role of the extra 2′‐OH groups. Furthermore, our computations present new insights on why the cation is required for self‐assembly: unexpectedly the cation is not necessary to relieve the repulsion between the oxygen atoms in the central cavity, but it is needed to overcome the entropic penalty.

Direct Detection of the Ion Pair to Free Ions Transformation upon Complexation with an Ion Receptor in Non-Polar Solvents by using Conductometry

In this study, we performed conductometry in various organic solvents to directly detect the transformation from tetrabutylammonium chloride (TBACl) ion‐pair salt to the free ions through complexation with meso‐octamethylcalix[4]pyrrole (CP), which is a well‐known receptor for chloride anions. In the presence of CP, the conductivity of TBACl increases in various non‐polar solvents, indicating that complexation with CP enhances the ionic dissociation of TBACl in such non‐polar solvents. In other words, CP recognizes chloride as an ion‐paired salt as well as a free anion in non‐polar solvents. Additionally, the TBA(CP–Cl) complex exhibited a considerably lower ion‐pairing constant (K_ip) than TBACl in non‐polar solvents, resulting in enhanced conductivity. Based on these findings, we can conclude that complexation of an anion with a hydrophobic anion receptor will be useful for creating functional and stimuli‐responsive soft materials in organic solvents using coulombic forces.

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models

The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.

Source of Cooperativity in Halogen-Bonded Haloamine Tetramers

Inspired by the isostructural motif in α-bromoacetophenone oxime crystals, we investigated halogen-halogen bonding in haloamine quartets. Our Kohn-Sham molecular orbital and energy decomposition analysis reveal a synergy that can be traced to a charge-transfer interaction in the halogen-bonded tetramers. The halogen lone-pair orbital on one monomer donates electrons into the unoccupied σ*N-X orbital on the perpendicular N-X bond of the neighboring monomer. This interaction has local σ symmetry. Interestingly, we discovered a second, somewhat weaker donor-acceptor interaction of local π symmetry, which partially counteracts the aforementioned regular σ-symmetric halogen-bonding orbital interaction. The halogen-halogen interaction in haloamines is the first known example of a halogen bond in which back donation takes place. We also find that this cooperativity in halogen bonds results from the reduction of the donor-acceptor orbital-energy gap that occurs every time a monomer is added to the aggregate.

The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics

Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp (2) to sp (3), does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

Mixed adenine/guanine quartets with three trans-a2 Pt(II) (a=NH(3) or MeNH(2)) cross-links: linkage and rotational isomerism, base pairing, and loss of NH(3)

Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross-linked by three linear metal moieties such as trans-a2 Pt(II) (with a=NH3 or MeNH2 ) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)}2 ][(ClO4 )6 ]⋅3H2 O (1) (with 9-EtA=9-ethyladenine and 9-MeGH=9-methylguanine) was crystallized from water and found to adopt a flat Z-shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9-MeGH, a meander-like construct, trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)2 }][(ClO4 )6 ]⋅[(9-MeGH)2 ]⋅7 H2 O (2) is formed, in which the two extra 9-MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1. Compound 1, and likewise the analogous complex 1 a (with NH3 ligands only), undergo loss of an ammonia ligand and formation of NH4 (+) when dissolved in [D6 ]DMSO. From the analogy between the behavior of 1 and 1 a it is concluded that a NH3 ligand from the central Pt atom is lost. Addition of 1-methylcytosine (1-MeC) to such a DMSO solution reveals coordination of 1-MeC to the central Pt. In an analogous manner, 9-MeGH can coordinate to the central Pt in [D6 ]DMSO. It is proposed that the proton responsible for formation of NH4 (+) is from one of the exocyclic amino groups of the two adenine bases, and furthermore, that this process is accompanied by a conformational change of the cation from Z-form to U-form. DFT calculations confirm the proposed mechanism and shed light on possible pathways of this process. Calculations show that rotational isomerism is not kinetically hindered and that it would preferably occur previous to the displacement of NH3 by DMSO. This displacement is the most energetically costly step, but it is compensated by the proton transfer to NH3 and formation of U(-H(+) ) species, which exhibits an intramolecular hydrogen bond between the deprotonated N6H(-) of one adenine and the N6H2 group of the other adenine. Finally the question is examined, how metal cross-linking patterns in closed metallacyclic quartets containing two adenine and two guanine nucleobases influence the overall shape (square, rectangle, trapezoid) and the planarity of a metalated purine quartet.

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)₂ <d(CpA)₂ <d(ApT)₂ <d(ApA)₂ <d(GpT)₂ <d(GpA)₂ <d(ApG)₂ <d(CpG)₂ <d(GpG)₂ <d(GpC)₂, where the energy differences between the last four dimers, d(ApG)₂, d(CpG)₂, d(GpG)₂ and d(GpC)₂, is within 4.0 kcal mol⁻¹, and the energy between the most and the least stable isomers is 13.4 kcal mol⁻¹. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.

Heteroditopic receptors for ion-pair recognition

Ion-pair recognition is a new field of research emerging from cation and anion coordination chemistry. Specific types of heteroditopic receptor designs for ion pairs and the complexity of ion-pair binding are discussed to illustrate key concepts such as cooperativity. The importance of this area of research is reflected by the wide variety of potential applications of ion-pair receptors, including applications as membrane transport and salt solubilization agents and sensors.

Aromatic and aliphatic CH hydrogen bonds fight for chloride while competing alongside ion pairing within triazolophanes

Triazolophanes are used as the venue to compete an aliphatic propylene CH hydrogen-bond donor against an aromatic phenylene one. Longer aliphatic C-H...Cl(-) hydrogen bonds were calculated from the location of the chloride within the propylene-based triazolophane. The gas-phase energetics of chloride binding (ΔG(bind) , ΔH(bind) , ΔS(bind) ) and the configurational entropy (ΔS(config) ) were computed by taking all low-energy conformations into account. Comparison between the phenylene- and propylene-based triazolophanes shows the computed gas-phase free energy of binding decreased from ΔG(bind) =-194 to -182 kJ mol(-1) , respectively, with a modest enthalpy-entropy compensation. These differences were investigated experimentally. An (1) H NMR spectroscopy study on the structure of the propylene triazolophane's 1:1 chloride complex is consistent with a weaker propylene CH hydrogen bond. To quantify the affinity differences between the two triazolophanes in dichloromethane, it was critical to obtain an accurate binding model. Four equilibria were identified. In addition to 1:1 complexation and 2:1 sandwich formation, ion pairing of the tetrabutylammonium chloride salt (TBA(+) ⋅Cl(-) ) and cation pairing of TBA(+) with the 1:1 triazolophane-chloride complex were observed and quantified. Each complex was independently verified by ESI-MS or diffusion NMR spectroscopy. With ion pairing deconvoluted from the chloride-receptor binding, equilibrium constants were determined by using (1) H NMR (500 μM) and UV/Vis (50 μM) spectroscopy titrations. The stabilities of the 1:1 complexes for the phenylene and propylene triazolophanes did not differ within experimental error, ΔG=(-38±2) and (-39±1) kJ mol(-1) , respectively, as verified by an NMR spectroscopy competition experiment. Thus, the aliphatic CH donor only revealed its weaker character when competing with aromatic CH donors within the propylene-based triazolophane.