Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H ⋯ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H ⋯ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H ⋯ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels

The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous work, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations was introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (∼20 fold) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases.

Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands

Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the arginine-bound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.

Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage

Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.