High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs

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.

Quantum Effects Explain the Twist Angle in the Helical Structure of DNA

Why are DNA bases stacked in a double helix structure? We combined three theoretical approaches to demonstrate how one core concept derived from quantum mechanics (Pauli repulsion) annihilates the contribution of dispersion to the π-π stacking. The helical architecture is governed by a combination of exchange and electrostatic forces, a result that is interpreted from both a computational and a biological perspective.

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.

Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson-Crick/Hoogsteen Base Pairs: A Computational Analysis

The adsorption of 5-fluorouracil (5FU) on Watson-Crick (WC) base pairs and Hoogsteen (HT) base pairs has been studied using the dispersion-corrected density functional theory (DFT). The adsorption, binding energy, and thermochemistry for the drug 5FU on the WC and HT base pairs were determined. The most stable geometries were near planar geometry, and 5FU has a higher preference for WC than HT base pairs. The adsorption energies of 5FU on nucleobase pairs are consistently higher than pristine nucleobase pairs, indicating that nucleobase pair cleavage is less likely during the adsorption of the 5FU drug. The enthalpy change for the formation of 5FU-DNA base pairs is higher than that for the formation of 5FU-nucleobases and is enthalpy-driven. The E gap of AT base pairs is higher, suggesting that their chemical reactivity toward further reaction would be less than that of GC base pairs. The electron density difference (EDD) analysis shows a significant decrease in electron density in aromatic regions on the purine bases (adenine/guanine) compared to the pyrimidine bases. The MESP diagram of the stable 5FU-nucleobase pair complexes shows a directional interaction, with the positive regions in a molecule interacting with the negative region of other molecules. The atoms in molecule analysis show that the ρ(r) values of C=O···H-N are higher than those of N···H/N-H···O. The N···H intermolecular bonds between the base pair/drug and nucleobases are weak, closed shell interactions and are electrostatic in nature. The noncovalent interaction analysis shows that several new spikes are engendered along with an increase in their strength, which indicates that the H-bonding interactions are stronger and play a dominant role in stabilizing the complexes. Energy decomposition analysis shows that the drug-nucleobase pair complex has a marginal increase in the electrostatic contributions compared to nucleobase pair complexes.

DNA as a perfect quantum computer based on the quantum physics principles

DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band π -molecular orbital ( π -MO). The MO wave function ( Φ ) is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.