Strengthened cooperativity of DNA-based cyclic hydrogen-bonded rosettes by subtle functionalization

Cooperative effects cause extra stabilization of hydrogen-bonded supramolecular systems. In this work we have designed hydrogen-bonded rosettes derived from a guanine-cytosine Janus-type motif with the aim of finding a monomer that enhances the synergy of supramolecular systems. For this, relativistic dispersion-corrected density functional theory computations have been performed. Our proposal involves a monomer with three hydrogen-bonds pointing in the same direction, which translates into shorter bonds, stronger donor-acceptor interactions, and more attractive electrostatic interactions, thus giving rise to rosettes with strengthened cooperativity. This newly designed rosette has triple the cooperativity found for the naturally occurring guanine quadruplex.

The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond

The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.

Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems

The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.

Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex

Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.

Hydrogen and Halogen Bonding in Homogeneous External Electric Fields: Modulating the Bond Strengths

Recent years have witnessed various fascinating phenomena arising from the interactions of noncovalent bonds with homogeneous external electric fields (EEFs). Here we performed a computational study to interpret the sensitivity of intrinsic bond strengths to EEFs in terms of steric effect and orbital interactions. The block-localized wavefunction (BLW) method, which combines the advantages of both ab initio valence bond (VB) theory and molecular orbital (MO) theory, and the subsequent energy decomposition (BLW-ED) approach were adopted. The sensitivity was monitored and analyzed using the induced energy term, which is the variation in each energy component along the EEF strength. Systems with single or multiple hydrogen (H) or halogen (X) bond(s) were also examined. It was found that the X-bond strength change to EEFs mainly stems from the covalency change, while generally the steric effect rules the response of H-bonds to EEFs. Furthermore, X-bonds are more sensitive to EEFs, with the key difference between H- and X-bonds lying in the charge transfer interaction. Since phenylboronic acid has been experimentally used as a smart linker in EEFs, switchable sensitivity was scrutinized with the example of the phenylboronic acid dimer, which exhibits two conformations with either antiparallel or parallel H-bonds, thereby, opposite or consistent responses to EEFs. Among the studied systems, the quadruple X-bonds in molecular capsules exhibit remarkable sensitivity, with its interaction energy increased by -95.2 kJ mol^-1 at the EEF strength 0.005 a.u.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds

Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.

Halogen Bonding: An Odd Chemistry?

Halogen bonding is a flourishing field of research, but has for long been little recognized. The same goes for its scientific hero, Odd Hassel, who laid the foundations for all current developments. The crystallographic observation of halogen-oxygen interatomic distances shorter than the sum of the van der Waals radii of the involved atoms, and the interpretation of this phenomenon as a charge-transfer interaction, have been ground-breaking. Today, charge-transfer to a polarized halogen is not any longer seen as "odd", but is commonly referred to as halogen bonding, and is widely exploited in chemistry. Despite the recognition of Hassel's work with a Nobel prize in 1969, surprisingly little appreciation is given to date to the devoted scientist, who established a world-leading laboratory during one of the darkest eras of history. Herein, we wish to revive the legacy and highlight the impact of Odd Hassel's ground-breaking discoveries.

Learning to Model G-Quadruplexes: Current Methods and Perspectives

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.

Synthesis and characterization of N-heterocyclic carbene-MOEt2 complexes (M = Cu, Ag, Au). Analysis of solvated auxiliary-ligand free [(NHC)M]+ species

We report the synthesis, characterization and computational analysis of coinage metal-ether complexes supported by N-heterocyclic carbenes (NHC), SIPr and Et2CAAC. The related water adducts are also included. The [(NHC)M]+(M = Cu, Ag, Au) species show the noteworthy ability to bind Et2O and H2O. This interaction towards Et2O and H2O is partly ascribed to a σ-hole bonding with an almost linear disposition, taking advantage of the enhanced σ-hole potential evaluated for such [(NHC)M]+ species. This enhanced ability is larger than those found for non-covalent interactions involving main group species.

Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA

To gain better understanding of the stabilizing interactions between metal ions and DNA quadruplexes, dispersion-corrected density functional theory (DFT-D) based calculations were performed on double-, triple- and four-layer guanine tetrads interacting with alkali metal cations. All computations were performed in aqueous solution that mimics artificial supramolecular conditions where guanine bases assemble into stacked quartets as well as biological environments in which telomeric quadruplexes are formed. To facilitate the computations on these significant larger systems, optimization of the DFT description was performed first by evaluating the performance of partial reduced basis sets. Analysis of the stabilizing interactions between alkali cations and the DNA bases in double and triple-layer guanine quadruplex DNA reproduced the experimental affinity trend of the order Li⁺< Rb⁺ < Na⁺ < K⁺. The desolvation and the size of alkali metal cations are thought to be responsible for the order of affinity. Nevertheless, for the alkali metal cation species individually, the magnitude of the bond energy stays equal for binding as first, second or third cation in double, triple and four-layer guanine quadruplexes, respectively. This is the result of an interplay between a decreasingly stabilizing interaction energy and increasingly stabilizing solvation effects, along the consecutive binding events. This diminished interaction energy is the result of destabilizing electrostatic repulsion between the hosted alkali metal cations. This work emphasizes the stabilizing effect of aqueous solvent on large highly charged biomolecules.

Stabilizing solvent effects and electrostatic repulsion are responsible for the constant alkali metal cation affinity in multi-layer guanine quadruplexes.

Lack of Cooperativity in the Triangular X3 Halogen-Bonded Synthon?

We have investigated 44 crystal structures, found in the Cambridge Structural Database, containing the X₃ synthon (where X = Cl, Br, I) in order to verify whether three type II halogen-halogen contacts forming the synthon exhibit cooperativity. A hypothesis that this triangular halogen-bonded motif is stabilized by cooperative effects is postulated on the basis of structural data. However, theoretical investigations of simplified model systems in which the X₃ motif is present demonstrate that weak synergy occurs only in the case of the I₃ motif. In the present paper we computationally investigate crystal structures in which the X₃ synthon is present, including halomesitylene structures, that are usually described as being additionally stabilized by a synergic interaction. Our computations find no cooperativity for halomesitylene trimers containing the X₃ motif. Only in the case of two other structures containing the I₃ synthon a very weak or weak synergy, i.e. the cooperative effect being stronger than -0.40 kcal mol^-1, is found. The crystal structure of iodoform has the most pronounced cooperativity of all investigated systems, amounting to about 10% of the total interaction energy.

Halogen-bonded haloamine trimers - modelling the X3 synthon

Halogen-halogen bonded haloamine trimers serve as model systems for the X3 synthon present in numerous crystal structures and in two-dimensional self-assembled nanoarchitectures. Halogen bonds forming the synthon are often considered to display cooperativity. Synergy effects were previously found for halogen-halogen bonded bromoamine and iodoamine tetramers. In the present study comparison between haloamine cyclic trimers and tetramers is made. The cooperativity occurring in bromoamine and iodoamine clusters is significantly weaker in the case of the trimers. The present study demonstrates that the bromoamine and iodoamine trimers display weaker cooperativity due to a smaller number of synergy components in comparison to the corresponding tetramers of stronger cooperativity. Moreover, the halogen-halogen interactions in bromoamine and iodoamine dimers with the geometries of the corresponding trimers and tetramers are examined using energy decomposition analysis methods (supermolecular, canonical EDA and SAPT) and the Kohn-Sham molecular orbital model. The results of the analysis indicate that although the interaction energy values for the dimers of the different spatial arrangement are very close to each other, their origin is substantially different. For pairs with the geometry of the trimers orbital interactions and electrostatic attraction are both weaker than for the corresponding dimers with the geometry of the tetramers. This is especially important because both donor-acceptor interactions and electrostatic attraction were previously proven to be responsible for cooperative effects occurring in the bromoamine and iodoamine tetramers.

Strengthening of halogen bond in XCl∙∙∙FH∙∙∙F- through cooperativity with a strong hydrogen bond and proton transfer

A theoretical calculation has been performed for the ternary complexes XCl∙∙∙FH∙∙∙F^- (X = CCH, CN, OH, NC, and F) and the corresponding binary complexes. The halogen bond in the dyad is very weak with the interaction energy less than 2.5 kcal/mol. Interestingly, the halogen bond gets a big enhancement when it combines with a very strong hydrogen bond in FH∙∙∙F^-, and the largest interaction energy is up to ∼25.6 kcal/mol in FCl∙∙∙FH∙∙∙F^-. The enhancement of halogen bond not only results in a larger elongation of X-Cl bond and a bigger redshift of the bond stretch vibration but also makes the blue-shifting halogen bond in NCCl∙∙∙FH be a red-shifting one in NCCl∙∙∙FH∙∙∙F^-. The halogen bond belongs to a purely close-shell interaction in the dyad, while it becomes a partially covalent interaction in XCl∙∙∙FH∙∙∙F^- (X = OH, NC, and F) with negative energy density. In FH∙∙∙F^-, the proton is shared between the two F atoms, however, this proton transfers towards the F^- end in XCl∙∙∙FH∙∙∙F^-.

"Anti-Electrostatic" Halogen Bonding

Halogen bonding is often described as being driven predominantly by electrostatics, and thus adducts between anionic halogen bond (XB) donors (halogen-based Lewis acids) and anions seem counterintuitive. Such "anti-electrostatic" XBs have been predicted theoretically but for organic XB donors, there are currently no experimental examples except for a few cases of self-association. Reported herein is the synthesis of two negatively charged organoiodine derivatives that form anti-electrostatic XBs with anions. Even though the electrostatic potential is universally negative across the surface of both compounds, DFT calculations indicate kinetic stabilization of their halide complexes in the gas phase and particularly in solution. Experimentally, self-association of the anionic XB donors was observed in solid-state structures, resulting in dimers, trimers, and infinite chains. In addition, co-crystals with halides were obtained, representing the first cases of halogen bonding between an organic anionic XB donor and a different anion. The bond lengths of all observed interactions are 14-21 % shorter than the sum of the van der Waals radii.

Is There a Single Ideal Parameter for Halogen-Bonding-Based Lewis Acidity?

Halogen-bond donors (halogen-based Lewis acids) have now found various applications in diverse fields of chemistry. The goal of this study was to identify a parameter obtainable from a single DFT calculation that reliably describes halogen-bonding strength (Lewis acidity). First, several DFT methods were benchmarked against the CCSD(T) CBS binding data of complexes of 17 carbon-based halogen-bond donors with chloride and ammonia as representative Lewis bases, which revealed M05-2X with a partially augmented def2-TZVP(D) basis set as the best model chemistry. The best single parameter to predict halogen-bonding strengths was the static σ-hole depth, but it still provided inaccurate predictions for a series of compounds. Thus, a more reliable parameter, Ωσ* , has been developed through the linear combination of the σ-hole depth and the σ*(C-I) energy, which was further validated against neutral, cationic, halogen- and nitrogen-based halogen-bond donors with very good performance.

Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest

Essential to understanding life, the biomolecular phenomena have been an important subject in science, therefore a necessary path to be covered to make progress in human knowledge. To fully comprehend these processes, the non-covalent interactions are the key. In this review, we discuss how specific protein-ligand interactions can be efficiently described by low computational cost methods, such as Molecular Mechanics (MM). We have taken as example the case of the halogen bonds (XB). Albeit generally weaker than the hydrogen bonds (HB), the XBs play a key role to drug design, enhancing the affinity and selectivity toward the biological target. Along with the attraction between two electronegative atoms in XBs explained by the σ-hole model, important orbital interactions, as well as relief of Pauli repulsion take place. Nonetheless, such electronic effects can be only well-described by accurate quantum chemical methods that have strong limitations dealing with supramolecular systems due to their high computational cost. To go beyond the poor description of XBs by MM methods, reparametrizing the force-fields equations can be a way to keep the balance between accuracy and computational cost. Thus, we have shown the steps to be considered when parametrizing force-fields to achieve reliable results of complex non-covalent interactions at MM level for In Silico drug design methods.

A Crystallographic Charge Density Study of the Partial Covalent Nature of Strong N⋅⋅⋅Br Halogen Bonds

The covalent nature of strong N-Br⋅⋅⋅N halogen bonds in a cocrystal (2) of N-bromosuccinimide (NBS) with 3,5-dimethylpyridine (lut) was determined from X-ray charge density studies and compared to a weak N-Br⋅⋅⋅O halogen bond in pure crystalline NBS (1) and a covalent bond in bis(3-methylpyridine)bromonium cation (in its perchlorate salt (3). In 2, the donor N-Br bond is elongated by 0.0954 Å, while the Br⋅⋅⋅acceptor distance of 2.3194(4) is 1.08 Å shorter than the sum of the van der Waals radii. A maximum electron density of 0.38 e Å^-3 along the Br⋅⋅⋅N halogen bond indicates a considerable covalent contribution to the total interaction. This value is intermediate to 0.067 e Å^-3 for the Br⋅⋅⋅O contact in 1, and approximately 0.7 e Å^-3 in both N-Br bonds of the bromonium cation in 3. A calculation of the natural bond order charges of the contact atoms, and the σ*(N1-Br) population of NBS as a function of distance between NBS and lut, have shown that charge transfer becomes significant at a Br⋅⋅⋅N distance below about 3 Å.

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.

Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions?

Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.

Modulating the intrinsic reactivity of molecules through non-covalent interactions

Non-covalent interactions as tools for modifying molecular properties.

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.

The effect of anions on noncovalent interactions in model clusters of chalcogen-containing (CH3)2X (X = O, S, Se) molecules

A computational study of F⁻⋯(CH₃)₂O⋯CH₃F with F⁻ bound to the protons of the two methyl groups, found significant enhancement of the O⋯C interaction relative to the neutral (CH₃)₂O⋯CH₃F dyad.

Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis

Variational energy decomposition analysis establishes charge-transfer as the origin of halogen bond strength differences that go against electrostatics.

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)_nn ≤ 5.

Modified Guanines as Constituents of Smart Ligands for Nucleic Acid Quadruplexes

Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining genome stability and the cell life cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that guanine-based ligands with a porphyrin core can be used as markers of G-quadruplex assemblies in cell tissues. Herein, model systems of guanine-based ligands are explored by DFT methods. The energies of formation of modified guanine tetrads and those of modified tetrads stacked on the top of natural guanine tetrads have been calculated. The interaction energy has been decomposed into contributions from hydrogen bonding, stacking, and ion coordination and a twist-rise potential energy scan has been performed to find the individual local minima. Energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2 ) on individual energy terms. In addition, cooperative reinforcement in forming the modified and stacked tetrads, as well as the frontier orbitals participating in the hydrogen-bonding framework involving the HOMO-LUMO gap between the occupied σHOMO on the proton-accepting C=O and =N- groups and unoccupied σLUMO on the N-H groups, has been studied. The investigated systems are demonstrated to have a potential in ligand development, mainly due to stacking enhancement compared with natural guanine, which is used as a reference.

Asymmetric bifurcated halogen bonds

Halogen bonding (XB) is being extensively explored for its potential use in advanced materials and drug design. Despite significant progress in describing this interaction by theoretical and experimental methods, the chemical nature remains somewhat elusive, and it seems to vary with the selected system. In this work we present a detailed DFT analysis of three-center asymmetric halogen bond (XB) formed between dihalogen molecules and variously 4-substituted 1,2-dimethoxybenzene. The energy decomposition, orbital, and electron density analyses suggest that the contribution of electrostatic stabilization is comparable with that of non-electrostatic factors. Both terms increase parallel with increasing negative charge of the electron donor molecule in our model systems. Depending on the orientation of the dihalogen molecules, this bifurcated interaction may be classified as 'σ-hole - lone pair' or 'σ-hole - π' halogen bonds. Arrangement of the XB investigated here deviates significantly from a recent IUPAC definition of XB and, in analogy to the hydrogen bonding, the term bifurcated halogen bond (BXB) seems to be appropriate for this type of interaction.

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.

How amino and nitro substituents direct electrophilic aromatic substitution in benzene: an explanation with Kohn–Sham molecular orbital theory and Voronoi deformation density analysis

Molecular orbitals of aniline explain electrophilic substitution, whereas for nitrobenzene charge rearrangements are needed.

The role of alkali metal cations in the stabilization of guanine quadruplexes: why K+ is the best

The desolvation and size of monovalent alkali metal ions are of equal importance for the cation affinity of guanine quadruplexes.

The activation strain model and molecular orbital theory

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔE_strain(ζ) + ΔE_int(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324-343. doi: 10.1002/wcms.1221.