Quantum and classical effects in DNA point mutations: Watson-Crick tautomerism in AT and GC base pairs

Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials

Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions. We perform ab initio (PBE0/6-31G*) quantum mechanical/molecular mechanical (QM/MM) simulations to examine the free energy surface for tautomerization. We demonstrate that while the ab initio QM/MM simulations are accurate, considerable sampling is required to achieve high precision in the free energy barriers. To address this problem, we develop a QM/MM machine learning potential correction (QM/MM-ΔMLP) that is able to improve the computational efficiency, greatly extend the accessible time scales of the simulations, and enable practical application of path integral molecular dynamics to examine nuclear quantum effects. We find that the inclusion of nuclear quantum effects has only a modest effect on the mechanistic pathway but leads to a considerable lowering of the free energy barrier for the GT*⇌G*T equilibrium. Our results enable a rationalization of observed experimental data and the prediction of populations of rare tautomeric forms of nucleobases and rates of their interconversion in B-DNA.

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS

The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.

Multiscale simulations reveal the role of PcrA helicase in protecting against spontaneous point mutations in DNA

Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G[Formula: see text]C[Formula: see text]) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.

Quantum Biology and the Potential Role of Entanglement and Tunneling in Non-Targeted Effects of Ionizing Radiation: A Review and Proposed Model

It is well established that cells, tissues, and organisms exposed to low doses of ionizing radiation can induce effects in non-irradiated neighbors (non-targeted effects or NTE), but the mechanisms remain unclear. This is especially true of the initial steps leading to the release of signaling molecules contained in exosomes. Voltage-gated ion channels, photon emissions, and calcium fluxes are all involved but the precise sequence of events is not yet known. We identified what may be a quantum entanglement type of effect and this prompted us to consider whether aspects of quantum biology such as tunneling and entanglement may underlie the initial events leading to NTE. We review the field where it may be relevant to ionizing radiation processes. These include NTE, low-dose hyper-radiosensitivity, hormesis, and the adaptive response. Finally, we present a possible quantum biological-based model for NTE.

Investigating the Spectroscopy of the Gas Phase Guanine-Cytosine Pair: Keto versus Enol Configurations

We report on a vibrational study of the guanine-cytosine dimer tautomers using state-of-the-art quasiclassical trajectory and semiclassical vibrational spectroscopy. The latter includes possible quantum mechanical effects. Through an accurate comparison to the experimental spectra, we are able to shine a light on the hydrogen bond network of one of the main subunits of DNA and put the experimental assignment on a solid footing. Our calculations corroborate the experimental conclusion that the global minimum Watson-and-Crick structure is not detected in the spectra, and there is no evidence of tunnel-effect-based double proton hopping. Our accurate assignment of the spectral features may also serve as a basis for the development of precise force fields to study the guanine-cytosine dimer.

Tautomerism and Rotamerism of Favipiravir and Halogenated Analogues in Solution and in the Solid State

Favipiravir is an important selective antiviral against RNA-based viruses, and currently, it is being repurposed as a potential drug for the treatment of COVID-19. This type of chemical system presents different carboxamide-rotameric and hydroxyl-tautomeric states, which could be essential for interpreting its selective antiviral activity. Herein, the tautomeric 3-hydroxypyrazine/3-pyrazinone pair of favipiravir and its 6-substituted analogues, 6-Cl, 6-Br, 6-I, and 6-H, were fully investigated in solution and in the solid state through ultraviolet-visible, 1H nuclear magnetic resonance, infrared spectroscopy, and X-ray diffraction techniques. Also, a study of the gas phase was performed using density functional theory calculations. In general, the keto-enol balance in these 3-hydroxy-2-pyrazinecarboxamides is finely modulated by external and internal electrical variations via changes in solvent polarity or by replacement of substituents at position 6. The enol tautomer was prevalent in an apolar environment, whereas an increase in the level of the keto tautomer was favored by an increase in solvent polarity and, even moreso, with a strong hydrogen-donor solvent. Keto tautomerization was favored either in solution or in the solid state with a decrease in 6-substituent electronegativity as follows: H ≫ I ≈ Br > Cl ≥ F. Specific rotameric states based on carboxamide, "cisoide" and "transoide", were identified for the enol and keto tautomer, respectively; their rotamerism is dependent on the tautomerism and not the aggregation state.

DNA hydrogels and nanogels for diagnostics, therapeutics, and theragnostics of various cancers

As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years. The main contributor to this is the programmability of these 3-dimensional (3D) scaffolds that creates fundamental effects, especially in treating cancer diseases. Like other active biological ingredients (ABIs), DNA hydrogels can be functionalized with other active agents that play a role in targeting drug delivery and modifying the half-life of the therapeutic cargoes in the body's internal environment. Considering the brilliant advantages of DNA hydrogels, in this survey, we intend to submit an informative collection of feasible methods for the design and preparation of DNA hydrogels and nanogels, and the responsivity of the immune system to these therapeutic cargoes. Moreover, the interactions of DNA hydrogels with cancer biomarkers are discussed in this account. Theragnostic DNA nanogels as an advanced species for both detection and therapeutic purposes are also briefly reviewed.

A critical appraisal of the relative contribution of tissue architecture, genetics, epigenetics and cell metabolism to carcinogenesis

Here we contrast several carcinogenesis models. The somatic-mutation-theory posits mutations as main causes of malignancy. However, inconsistencies led to alternative explanations. For example, the tissue-organization-field-theory considers disrupted tissue-architecture as main cause. Both models can be reconciled using systems-biology-approaches, according to which tumors hover in states of self-organized criticality between order and chaos, are emergent results of multiple deviations and are subject to general laws of nature: inevitable variation(mutation) explainable by increased entropy(second-law-of-thermodynamics) or indeterminate decoherence upon measurement of superposed quantum systems(quantum mechanics), followed by Darwinian-selection. Genomic expression is regulated by epigenetics. Both systems cooperate. So cancer is neither just a mutational nor an epigenetic problem. Rather, epigenetics links environmental cues to endogenous genetics engendering a regulatory machinery that encompasses specific cancer-metabolic-networks. Interestingly, mutations occur at all levels of this machinery (oncogenes/tumor-suppressors, epigenetic-modifiers, structure-genes, metabolic-genes). Therefore, in most cases, DNA mutations may be the initial and crucial cancer-promoting triggers.

Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy

The level of interest in probing the strength of noncovalent interactions in DNA duplexes is high, as these weak forces dictate the range of suprastructures the double helix adopts under different conditions, in turn directly impacting the biological functions and industrial applications of duplexes that require making and breaking them to access the genetic code. However, few experimental tools can measure these weak forces embedded within large biological suprastructures in the native solution environment. Here, we develop experimental methods for detecting the presence of a single noncovalent interaction [a hydrogen bond (H-bond)] within a large DNA duplex in solution and measure its formation enthalpy (ΔH_f). We report that introduction of a H-bond into the TC2═O group from the noncanonical nucleobase 2-aminopurine produces an expected decrease ∼10 ± 0.76 cm^-1 (from ∼1720 cm^-1 in Watson-Crick to ∼1710 cm^-1 in 2-aminopurine), which correlates with an enthalpy of ∼0.93 ± 0.066 kcal/mol for this interaction.

How proton transfer impacts hachimoji DNA

Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson-Crick DNA due to the barrier for Z-P and S-B being 30% lower than in G-C and A-T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate.

Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair during DNA Strand Separation

The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the time scales and dynamics of DNA strand separation and the statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerization reaction. We propose that DNA strand separation allows the stable tautomerization of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.

Tunneling Effect in Proton Transfer: Transfer Matrix Approach

The transfer matrix (TM) method was applied to calculate the transmission probability (TP) for proton transfer reactions. The tunneling factors in the reaction rate constants were also evaluated using the TPs. To test this method, TPs for the Eckart potentials modeled as a guanine-cytosine base pair were calculated by the TM method and compared to TPs by the analytical solution. As a result, the errors in the TPs by the TM method were quite small. The tunneling factors for the guanine-thymine (G-T) and adenine-cytosine (A-C) mispair reactions were then evaluated by the TM method. A shoulder appears on each potential for these reactions [Odai, K.; Umesaki,K. J. Phys. Chem. A. 2021, 125, 8196-8204]. As a result, the shoulder for the G-T mispair reaction contributes significantly to the tunneling, while the shoulder for the A-C mispair reaction contributes little to the tunneling. These results are difficult to obtain with methods such as Wigner's tunneling factor.

Tautomeric Equilibrium in 1-Benzamidoisoquinoline Derivatives

In this study, the tautomeric equilibrium of a sequence of 1-benzamidoisoquinoline derivatives was investigated with the tools of NMR spectroscopy and computational chemistry. The equilibrium between different tautomers in these systems could be controlled via the substitution effect, and the relative content of the amide form varied from 74% for the strong electron-donating NMe2 substituent to 38% for the strong electron-accepting NO2 group in the phenyl ring. In contrast to the previously investigated 2-phenacylquinoline derivatives, the most stable and thus most abundant tautomer in the 1-benzamidoisoquinoline series except the two most electron-accepting substituents was an amide. The intramolecular hydrogen bond present in the enol tautomer competed with the intermolecular hydrogen bonds created with the solvent molecules and thus was not a sufficient factor to favor this tautomer in the mixture. Although routinely computational studies of tautomeric equilibrium are performed within the continuum solvent models, it is proven here that the inclusion of the explicit solvent is mandatory in order to reproduce the experimental tendencies observed for this type of system, facilitating strong intermolecular hydrogen bonds.

Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism

The misincorporation of a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling first-principles quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our calculated rates of genetic error formation are in excellent agreement with experimental observations in DNA. Furthermore, our quantum mechanics/molecular mechanics model predicts the existence of a short-lived "tunnelling-ready" configuration along the wobble reaction pathway in the polymerase active site, dramatically increasing the rate of proton transfer by a hundredfold, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase.

Proton transfer during DNA strand separation as a source of mutagenic guanine-cytosine tautomers

Proton transfer between the DNA bases can lead to mutagenic Guanine-Cytosine tautomers. Over the past several decades, a heated debate has emerged over the biological impact of tautomeric forms. Here, we determine that the energy required for generating tautomers radically changes during the separation of double-stranded DNA. Density Functional Theory calculations indicate that the double proton transfer in Guanine-Cytosine follows a sequential, step-like mechanism where the reaction barrier increases quasi-linearly with strand separation. These results point to increased stability of the tautomer when the DNA strands unzip as they enter the helicase, effectively trapping the tautomer population. In addition, molecular dynamics simulations indicate that the relevant strand separation time is two orders of magnitude quicker than previously thought. Our results demonstrate that the unwinding of DNA by the helicase could simultaneously slow the formation but significantly enhance the stability of tautomeric base pairs and provide a feasible pathway for spontaneous DNA mutations.

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 tunnelling in the context of SARS-CoV-2 infection

The SARS-CoV-2 pandemic has added new urgency to the study of viral mechanisms of infection. But while vaccines offer a measure of protection against this specific outbreak, a new era of pandemics has been predicted. In addition to this, COVID-19 has drawn attention to post-viral syndromes and the healthcare burden they entail. It seems integral that knowledge of viral mechanisms is increased through as wide a research field as possible. To this end we propose that quantum biology might offer essential new insights into the problem, especially with regards to the important first step of virus-host invasion. Research in quantum biology often centres around energy or charge transfer. While this is predominantly in the context of photosynthesis there has also been some suggestion that cellular receptors such as olfactory or neural receptors might employ vibration assisted electron tunnelling to augment the lock-and-key mechanism. Quantum tunnelling has also been observed in enzyme function. Enzymes are implicated in the invasion of host cells by the SARS-CoV-2 virus. Receptors such as olfactory receptors also appear to be disrupted by COVID-19. Building on these observations we investigate the evidence that quantum tunnelling might be important in the context of infection with SARS-CoV-2. We illustrate this with a simple model relating the vibronic mode of, for example, a viral spike protein to the likelihood of charge transfer in an idealised receptor. Our results show a distinct parameter regime in which the vibronic mode of the spike protein enhances electron transfer. With this in mind, novel therapeutics to prevent SARS-CoV-2 transmission could potentially be identified by their vibrational spectra.

UVC radiation intensity dependence of pathogen decontamination rate: semiclassical theory and experiment

A semiclassical (light classical and molecule quantum) model describing the dependence of DNA/RNA dimerization rate as function of the ultraviolet C (UVC) radiation's intensity is proposed. Particularly, a nonlinear model is developed based on the Raman-like processes in quantum optics. The main result of the theory shows that the process of dimerization in the DNA/RNA depends strongly on the UVC light's intensity, thus proving a possible quantum microscopical mechanism of the interaction of UV light with the DNA. To corroborate the theoretical findings, we realize some experiments, by which want to investigate how the inactivation rate of the yeast colonies depends on the intensity of the UVC irradiation. The experimental results evidence a nonlinear decreasing of the residual yeast colonies as a function of the intensity in the irradiation process. The possibilities to optimize the intensity of UVC radiation in the considered decontamination equipment by using metamaterials are studied. The application of such equipment in disinfection of fluids (air, water, droplets, etc.), as well for the SARS-CoV-2-infected aerosols, is discussed.

Time delay during intra-base proton tunneling in the guanine base of the single stranded DNA

Spontaneous point mutations are one of the main actors in evolution, and the tautomerization of organic bases in the DNA is hypothesized to be the underlying mechanism of this crucial process. Tautomerization can be induced by proton tunneling, and if it occurs in single-stranded DNA (ssDNA) during the replication process, tautomerized bases might give rise to a mismatch, which will eventually defect the genetic code. In the present work, we report on the tautomerization time in the guanine base of the ssDNA. The model we use includes an intra-base tunneling mechanism such that time tunneling (delay time) is estimated to be around a few pico-seconds. The time delay is found to be biologically relevant which indicates that it is long enough to induce point mutations. Our results close a gap in the literature and sheds light on the importance of point mutations originating from quantum effects in the ssDNA.

The Selective Function of Quantum Biological Electron Transfer between DNA Bases and Metal Ions in DNA Replication

Metal ions play vital roles in the electron transfer between biological molecules in humans, animals, and plants. However, the electron transfer between metal ions and nucleic acids and its impact on DNA-ion binding during DNA replication has been ignored. Here, we present a long-range quantum biological electron transfer (QBET) between DNA bases and metal ions and its selective function of DNA-ion binding in DNA replication. We discover biophysical DNA-ion binding and create biological filters that allow selective DNA replication by dual modulators of the valence and concentration of metal ions. QBET-based DNA replication filters provide powerful tools for ultrasensitive polymerase chain reaction (PCR) to selectively amplify target sequences with a discrete concentration window of metal ions; for example, Au³⁺ exhibits a concentration window that is approximately 3 orders of magnitude lower than that of Na⁺. DNA-ion filters provide new perspectives into metal ion-mediated QBET in DNA replication and hold great potential in life sciences and medical applications.

General Designs Reveal a Purine-Pyrimidine Structural Code in Human DNA

The human genome carries a vast amount of information within its DNA sequences. The chemical bases A, T, C, and G are the basic units of information content, that are arranged into patterns and codes. Expansive areas of the genome contain codes that are not yet well understood. To decipher these, mathematical and computational tools are applied here to study genomic signatures or general designs of sequences. A novel binary components analysis is devised and utilized. This seeks to isolate the physical and chemical properties of DNA bases, which reveals sequence design and function. Here, information theory tools break down the information content within DNA bases, in order to study them in isolation for their genomic signatures and non-random properties. In this way, the RY (purine/pyrimidine), WS (weak/strong), and KM (keto/amino) general designs are observed in the sequences. The results show that RY, KM, and WS components have a similar and stable overall profile across all human chromosomes. It reveals that the RY property of a sequence is most distant from randomness in the human genome with respect to the genomic signatures. This is true across all human chromosomes. It is concluded that there exists a widespread potential RY code, and furthermore, that this is likely a structural code. Ascertaining this feature of general design, and potential RY structural code has far-reaching implications. This is because it aids in the understanding of cell biology, growth, and development, as well as downstream in the study of human disease and potential drug design.

Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs

DNA (2'-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in biology and disease. Despite being comprised primarily of only four cognate nucleobases, nucleic acids can adopt complex three-dimensional structures, and RNA in particular, can catalyze biochemical reactions to regulate a wide variety of biological processes. Such chemical versatility is due in part to the phenomenon of nucleobase tautomerism, whereby the bases can adopt multiple, yet distinct isomeric forms, known as tautomers. For nucleobases, tautomers refer to structural isomers that differ from one another by the position of protons. By altering the position of protons on nucleobases, many of which play critical roles for hydrogen bonding and base pairing interactions, tautomerism has profound effects on the biochemical processes involving nucleic acids. For example, the transient formation of minor tautomers during replication could generate spontaneous mutations. These mutations could arise from the stabilization of mismatches, in the active site of polymerases, in conformations involving minor tautomers that are indistinguishable from canonical base pairs. In this review, we discuss the evidence for tautomerism in DNA, and its consequences to the fidelity of DNA replication. Also reviewed are RNA systems, such as the riboswitches and self-cleaving ribozymes, in which tautomerism plays a functional role in ligand recognition and catalysis, respectively. We also discuss tautomeric nucleoside analogs that are efficacious as antiviral drug candidates such as molnupiravir for coronaviruses and KP1212 for HIV. The antiviral efficacy of these analogs is due, in part, to their ability to exist in multiple tautomeric forms and induce mutations in the replicating viral genomes. From a technical standpoint, minor tautomers of nucleobases are challenging to identify directly because they are rare and interconvert on a fast, millisecond to nanosecond, time scale. Nevertheless, many approaches including biochemical, structural, computational and spectroscopic methods have been developed to study tautomeric dynamics in RNA and DNA systems, and in antiviral nucleoside analogs. An overview of these methods and their applications is included here.

Structural analysis of dexrazoxane: Exploring tautomeric conformations

Structural analysis of dexrazoxane, as a cardioprotective agent, was done in this work by exploring formations of tautomeric conformations and investigating the corresponding effects. Density functional theory (DFT) calculations were performed to optimize the structures to evaluate their molecular and atomic descriptors. In addition to the original structure of dexrazoxane, eight tautomers were obtained with lower stability than the original compound. Movements of two hydrogen atoms in between nitrogen and oxygen atoms of heterocyclic ring put such significant effects. Moreover, electronic molecular orbital features showed effects of such tautomerism processes on distribution patterns and surfaces, in which evaluating the quadrupole coupling constants helped to show the role of atomic sites for resulting the features. As a consequence, the results indicated that the tautomeric formations could significantly change the features of dexrazoxane reminding the importance of carful medication of this drug for patients.

Atomistic mechanisms of the tautomerization of the G·C base pairs through the proton transfer: quantum-chemical survey

This study is devoted to the investigation of the G·C*^t_O2(WC)↔G*_NH3·C*^t(WC), G·C*_O2(WC)↔G*_NH3·C*(WC) and G*·C*_O2(WC)↔G*_NH3·C(w_WC)_↓ tautomerization reactions occurring through the proton transfer, obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in gas phase under normal conditions ('WC' means base pair in Watson-Crick configuration, T=298.15 K). These reactions lead to the formation of the G*_NH3·C*^t(WC), G*_NH3·C*(WC) and G*_NH3·C(w_WC)_↓ base pairs by the participation of the G*_NH3 base with NH₃ group. Gibbs free energies of activation for these reactions are 6.43, 11.00 and 1.63 kcal·mol^-1, respectively. All of these tautomerization reactions are dipole active. Finally, we believe that these non-dissociative processes, which are tightly connected with the tautomeric transformations of the G·C base pairs, play an outstanding role in supporting of the spatial structure of the DNA and RNA molecules with various functional purposes.

Time delay during the proton tunneling in the base pairs of the DNA double helix

DNA undergoes spontaneous point mutations, which are believed to be central to the evolution of the organisms and which are thought to occur by tautomerization of the canonical Guanine-Cytosine (G-C) base pair into non-canonical G∗-C∗ base pair via the double proton tunneling. In the present work, we close a gap in the literature by computing the time delay during the proton tunneling. Our results, based on the well-known dwell time and our model of the entropic time, range from femtoseconds to picoseconds, and completely agree with the time scales of the structural changes in molecules (mutation processes not the complete replication processes). The tunneling delay times are thus nonnegligible and imply that the DNA mutations can be resolved using the attosecond laser technology, if not the femtosecond technology. Our results can be relevant also for other tunneling-enabled biological processes.

Exploring chemistry features of favipiravir in octanol/water solutions

Favipiravir (Fav) has become a well-known drug for medication of patients by appearance of COVID-19. Heterocyclic structure and connected peptide group could make changes for Fav yielding different features from those required features. Therefore, it is indeed a challenging task to prepare a Fav compound with specific features of desired function. In this work, existence of eight Fav structures by tautomeric formations and peptide group rotations were obtained using density functional theory (DFT) optimization calculations. Gas phase, octanol solution, and water solution were employed to show impact of solution on features of Fav besides obtaining partition coefficients (LogP) for Fav compounds. Significant impacts of solutions were seen on features of Fav with the obtained LogP order: Fav-7 >  Fav-8 >  Fav-4 >  Fav-3 >  Fav-2 >  Fav-5 >  Fav-1 >  Fav-6. As a consequence, internal changes yielded significant impacts on features of Fav affirming its carful medication of COVID-19 patients.

Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.