Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

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.

New insights into the surface Enhanced Raman Scattering (SERS) response of adenine using chemometrics

The SERS response of adenine is one of the most studied, due to its outstanding exaltation. However, the spectra obtained strongly differ according to the experimental conditions and still remain not well understood. To be able to search for the presence of this molecule in complex environments, it is essential to better understand the SERS response of adenine alone. After a brief presentation of the literature on the subject, we present results suggesting that the experimental spectra would result from the overlap of different spectroscopic signatures, that may probably be due to different non-covalent interactions or different electromagnetic fields experienced by adenine molecules. An independent component analysis is reported. Our results underline the difficulty to precisely analyze the experimental data, the need to continue this research and to constitute data banks that would allow comparing the spectra obtained in different laboratories according to the experimental conditions.

Vibrational assignments of cyclic dimers and inter-monomers of adenine relating FT-IR, FT-Raman and UV spectra with SQMFF and DFT calculations

In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV-Visible spectra with hybrid B3LYP/6-311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm-1 have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm-1 are not due to N-H···N interactions but to bands of combination, as was previously suggested. The experimental available deuterated IR and terahertz spectra have allowed the complete assignments of regions of higher and lower wavenumbers. Good correlations were acquired comparing the theoretical IR, Raman and UV spectra of three species and the tetramer with the analogous experimental ones, suggesting the presence of all species in both phases. Vibronic bands are observed in the electronic spectra when adenine concentration is increased in aqueous solution evidencing the presence of monomer, tautomers and dimers, as reported by different studies. Similar characteristics of H bonds interactions are predicted for dimers 1 and 2 but different from the dimer 3, as revealed by using NBO and AIM calculations. Different scaled force constants values were found for the cyclic dimers 1 and 2, as compared to the corresponding to dimer 3.

Influence of the Solvent on the Stability of Aminopurine Tautomers and Properties of the Amino Group

Amino derivatives of purine (2-, 6-, 8-, and N-NH2) have found many applications in biochemistry. This paper presents the results of a systematic computational study of the substituent and solvent effects in these systems. The issues considered are the electron-donating properties of NH2, its geometry, π-electron delocalization in purine rings and tautomeric stability. Calculations were performed in ten environments, with 1 < ε < 109, using the polarizable continuum model of solvation. Electron-donating properties were quantitatively described by cSAR (charge of the substituent active region) parameter and π-electron delocalization by using the HOMA (harmonic oscillator model of aromaticity) index. In aminopurines, NH2 proximity interactions depend on its position and the tautomer. The results show that they are the main factor determining how solvation affects the electron-donating strength and geometry of NH2. Proximity with the NH∙∙∙HN repulsive interaction between the NH2 and endocyclic NH group results in stronger solvent effects than the proximity with two attractive NH∙∙∙N interactions. The effect of amino and nitro (previously studied) substitution on aromaticity was compared; these two groups have, in most cases, the opposite effect, with the largest being in N1H and N3H purine tautomers. The amino group has a smaller effect on the tautomeric preferences of purine than the nitro group. Only in 8-aminopurine do tautomeric preferences change: N7H is more stable than N9H in H2O.

Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.

Intramolecular Interactions in Derivatives of Uracil Tautomers

The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/−OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer).

Quantum Chemical Calculations with Machine Learning for Multipolar Electrostatics Prediction in RNA: An Application to Pentose

To develop a realistic electrostatic model that allows for the anisotropy of the atomic electron density, high-rank atomic multipole moments computed by quantum chemical calculations have been studied extensively. However, it is hard to process huge RNA systems only relying on quantum chemical calculations due to its highly computational cost. In this study, we employ five machine learning methods of Gaussian process regression with automatic relevance determination (ARDGPR), Kriging, radial basis function neural networks, Bagging, and generalized regression neural network to predict atomic multipole moments. Atom-atom electrostatic interaction energies are subsequently computed using the predicted atomic multipole moments in the pilot system pentose of RNA. Here, the performance of the five methods is compared in terms of both the multipole moment prediction errors and the electrostatic energy prediction errors. For the predicted high-rank multipole moments of the four elements (O, C, N, and H) in capped pentose, ARDGPR and Kriging consistently outperform the other three methods. Therefore, the multipole moments predicted by the two best methods of ARDGPR and Kriging are then used to predict electrostatic interaction energy of each pentose. Finally, the absolute average energy errors of ARDGPR and Kriging are 1.83 and 4.33 kJ mol^-1, respectively. Compared to Kriging, the ARDGPR method achieves a 58% decrease in the absolute average energy error. These satisfactory results demonstrated that the ARDGPR method with the strong feature extraction ability can predict the electrostatic interaction energy of pentose in RNA correctly and reliably.

Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers

Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2- or C8-) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8-X-substituted adenine systems may consist of a considerable amount of two tautomers-9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.

Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers

The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO2 group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers.

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.

Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs

The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods-DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)-are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers-e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented.

Impact of the Substituents on the Electronic Structure of the Four Most Stable Tautomers of Purine and Their Adenine Analogues

Substituent effects at the C2-, C8-, and N-positions of adenine and purine on the structural and π-electronic changes in their four tautomers were studied using the B97D3/aug-cc-pvdz computational level. The effect of various substituents (NO2, CN, CHO, Cl, F, H, Me, OMe, OH, and NH2) was characterized by the charge of the substituent active region (cSAR) approach and Hammett substituent constants σ. It has been found that for both adenine and purine derivatives, substituents from the C8-X position have a stronger influence on their electronic structure than from the C2-X and N-X positions. The presence of the amino group in adenine enhances the substituent effect compared to that which occurs in purine. In addition, its electronic structure is more sensitive to the effect of the substituent in 3H and 1H than in the 9H and 7H adenine tautomers. For a given substituent, a large variation in cSAR(X) values is observed, strongly dependent on the substitution position. For 7H and 9H adenine tautomers for C8-X systems, substituents reduce the aromaticity of the five-membered rings but increase the aromaticity of the six-membered rings.

Substituent effects on the stability of the four most stable tautomers of adenine and purine

Substituent effects at the C2-, C8- and N-positions of adenine and purine in their four the most stable tautomers are studied by means of B97D3/aug-cc-pvdz computation applying substituents of varying electronic properties: NO₂, CN, CHO, Cl, F, H, Me, OMe, OH and NH₂. The substituent effect is characterized by the substituent effect stabilization energy (SESE) and substituent Hammett constant σ. For adenine, SESE is obtained with purine as the reference system. Additionally, for both adenine and purine, SESE characteristics are estimated with benzene, imidazole and amino-pyrimidine as reference systems, when possible, taking into account substitution in topologically equivalent positions. The role of a C6-NH₂ group in adenine in modifying the substitution effect is observed and discussed. Additionally, the proximity effect for some asymmetric substituents (e.g. CHO, OMe) is recognized and meticulously analyzed.