Intriguing Intermolecular Interplay in Guanine Quartet Complexes with Alkali and Alkaline Earth Cations

Density functional theory study of crown ether-magnesium complexes: from a solvated ion to an ion trap

Metal ion detection rests on host-guest recognition. We propose a theoretical protocol for designing an optimal trap for a desired metal cation. A host for magnesium ions was sought for among derivatives of crown ethers 12-crown-4, 15-crown-5, and 18-crown-6. Mg-crown complexes and their hydrated counterparts with water molecules bound to the cation were optimized using density functional theory. Based on specific geometric criteria, Interacting quantum atoms analysis and density functional theory-based molecular dynamics of Mg-crown complexes immersed in water, crown ethers for optimal accommodation of Mg2+ in aqueous solution were identified. Selectivity of the chosen crowns towards Na+, K+, and Ca2+ ions is addressed.

Structural Insights into the Antiparallel G-Quadruplex in the Presence of K+ and Mg2+ Ions

G-Quadruplex (GQ) is a secondary structural unit of DNA, formed at the telomere region of the chromosome with a high guanine content. It is reported that the GQs can hinder many biological processes. Thus, research thrives to explore the structural stability of GQs. Studies based on circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments established the vital role of cations such as K⁺ and Mg²⁺ in the stability of antiparallel G-quadruplexes (AGQs). However, there is a need to understand how stability in AGQ is attained in the presence of cations. Here, we employed molecular dynamics (MD) simulations, steered MD (SMD) simulations, and QM/MM calculations to understand the biophysical and electronic bases of the stability imparted to AGQs via cation binding. Our results showed that Mg²⁺ prefers to bind in the plane with the guanine tetrad, whereas K⁺ binds in between the AGQ tetrads. Thus, three Mg²⁺ cations or two K⁺ ions are needed to stabilize an AGQ molecule, where each and every tetrad binds to Mg²⁺ more robustly with a higher binding affinity. SMD revealed that the traversal of K⁺ through the AGQ central channel required less force than that of Mg²⁺, illustrating the presence of more strong interactions between Mg²⁺ and AGQ tetrads compared to K⁺. The stabilization in the AGQ tetrads due to cation binding is reassessed by employing ab initio simulations. Mixed QM/MM calculations confirmed that Mg²⁺ binds strongly to AGQ compared to K⁺, and it induces higher interactions between the guanine tetrads. However, K⁺ binding to AGQ induces a higher stabilization energy than Mg²⁺ binding to AGQ tetrads. Despite the higher binding energy, Mg²⁺ binding imparts lower stabilization to AGQ due to its unfavorable fermionic quantum energy.

Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study

Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca²⁺, Sr²⁺ and Ba²⁺). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca²⁺ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.

Proton leap: shuttling of protons onto benzonitrile

The detailed description of chemical transformations in the interstellar medium allows deciphering the origin of a number of small and medium - sized organic molecules. We present density functional theory analysis of proton transfer from the trihydrogen cation and the ethenium cation to benzonitrile, a recently discovered species in the Taurus Molecular Cloud 1. Detailed energy transformations along the reaction paths were analyzed using the interacting quantum atoms methodology, which elucidated how the proton carrier influences the lightness to deliver the proton to benzonitrile's nitrogen atom. The proton carriers' deformation energy represents the largest destabilizing effect, whereas a proton's promotion energy, the benzonitrile-proton Coulomb attraction, as well as non-classical benzonitrile-proton and carrier-proton interaction are the dominant stabilizing energy components. As two ion-molecule reactions proceed without energy barriers, rate constants were estimated using the classical capture theory and were found to be an order of magnitude larger for the reaction with the trihydrogen cation compared to that with the ethenium cation (∼10^-8 and 10^-9 cm³ s^-1, respectively). These results were obtained both with quantum chemical and ab initio molecular dynamics simulations (the latter performed at 10 K and 100 K), confirming that up to 100 K both systems choose energetically undemanding routes by tracking the corresponding minimum energy paths. A concept of a turning point is introduced, which is an equivalent to the transition state in barrierless reactions.

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.

The significance of the metal cation in guanine-quartet – metalloporphyrin complexes

The distinct positions of the divalent metal ions with respect to the porphyrin ring are responsible for different interaction energies between metalloporphyrins and the guanine quartet.