The Role of Proton Transfer on Mutations

Further exploration of the physicochemical nature of μ2-bridge-relevant deprotonations via the elucidation of four kinds of alditol complexes

Single-crystal structures of four alditol complexes are presented. In LuCl3/galactitol and ScCl3/myo-inositol complexes, μ2-bridge-relevant deprotonations were observed. The polarization from two rare earth ions in the μ2-bridge activates the chemically inert OH and promotes deprotonation. Additionally, mass spectrometry, pH experiments, and quantum chemistry calculations were conducted to enhance our understanding of the μ2-bridge-relevant deprotonations. A common structural feature of the complexes where μ2-bridge-relevant deprotonation takes place is that two metal ions and two oxygen atoms in two μ2-bridges form an M2O2 cluster. The four atoms in the M2O2 cluster make up a parallelogram. Such a structure is useful to balance the strong coulombic repulsions between two M3+ and between two O-. In the ScCl3/myo-inositol complex, the deprotonation exhibits a characteristic of regional/chiral selectivity. Galactitol is a third alditol ligand where μ2-bridge-relevant deprotonation is observed. The flexible backbone of the galactitol allows the formation of more five-membered chelating rings and six-membered chelating rings, which are used to stabilize the rare earth ions of the μ2-bridge. The coordination makes the backbone of galactitol deviate from the zigzag conformation. The above results are helpful in the rational design of high-performance catalysts.

A review on point mutations via proton transfer in DNA base pairs in the absence and presence of electric fields

This comprehensive review focuses on spontaneous mutations that may occur during DNA replication, the fundamental process responsible for transferring genetic information. In 1963, Löwdin postulated that these mutations are primarily a result of proton transfer reactions within the hydrogen-bonded DNA base pairs. The single and double proton transfer reactions within the base pairs in DNA result in zwitterions and rare tautomers, respectively. For persistent mutations, these products must be generated at high rates and should be thermodynamically stable. This review covers the proton transfer reactions studied experimentally and computationally. The review also examines the influence of externally applied electric fields on the thermodynamics and kinetics of proton transfer reactions within DNA base pairs, and their biological implications.

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.

Systematic analysis of electronic barrier heights and widths for concerted proton transfer in cyclic hydrogen bonded clusters: (HF)n, (HCl)n and (H2O)n where n = 3, 4, 5

The MP2 and CCSD(T) methods are paired with correlation consistent basis sets as large as aug-cc-pVQZ to optimize the structures of the cyclic minima for (HF)n, (HCl)n and (H2O)n where n = 3-5, as well as the corresponding transition states (TSs) for concerted proton transfer (CPT). MP2 and CCSD(T) harmonic vibrational frequencies confirm the nature of each minimum and TS. Both conventional and explicitly correlated CCSD(T) computations are employed to assess the electronic dissociation energies and barrier heights for CPT near the complete basis (CBS) limit for all 9 clusters. Results for (HF)n are consistent with prior studies identifying Cnh and Dnh point group symmetry for the minima and TSs, respectively. Our computations also confirm that CPT proceeds through Cs TS structures for the C1 minima of (H2O)3 and (H2O)5, whereas the process goes through a TS with D2d symmetry for the S4 global minimum of (H2O)4. This work corroborates earlier findings that the minima for (HCl)3, (HCl)4 and (HCl)5 have C3h, S4 and C1 point group symmetry, respectively, and that the Cnh structures are not minima for n = 4 and 5. Moreover, our computations show the TSs for CPT in (HCl)3, (HCl)4 and (HCl)5 have D3h, D2d, and C2 point group symmetry, respectively. At the CCSD(T) CBS limit, (HF)4 and (HF)5 have the smallest electronic barrier heights for CPT (≈15 kcal mol-1 for both), followed by the HF trimer (≈21 kcal mol-1). The barriers are appreciably higher for the other clusters (around 27 kcal mol-1 for (H2O)4 and (HCl)3; roughly 30 kcal mol-1 for (H2O)3, (H2O)5 and (HCl)4; up to 38 kcal mol-1 for (HCl)5). At the CBS limit, MP2 significantly underestimates the CCSD(T) barrier heights (e.g., by ca. 2, 4 and 7 kcal mol-1 for the pentamers of HF, H2O and HCl, respectively), whereas CCSD overestimates these barriers by roughly the same magnitude. Scaling the barrier heights and dissociation energies by the number of fragments in the cluster reveals strong linear relationships between the two quantities and with the magnitudes of the imaginary vibrational frequency for the TSs.

Environment assisted quantum model for studying RNA-DNA-error correlation created due to the base tautomery

The adaptive mutation phenomenon has been drawing the attention of biologists for several decades in evolutionist community. In this study, we propose a quantum mechanical model of adaptive mutation based on the implications of the theory of open quantum systems. We survey a new framework that explain how random point mutations can be stabilized and directed to be adapted with the stresses introduced by the environments according to the microscopic rules dictated by constraints of quantum mechanics. We consider a pair of entangled qubits consist of DNA and mRNA pair, each coupled to a distinct reservoir for analyzing the spreed of entanglement using time-dependent perturbation theory. The reservoirs are physical demonstrations of the cytoplasm and nucleoplasm and surrounding environments of mRNA and DNA, respectively. Our predictions confirm the role of the environmental-assisted quantum progression of adaptive mutations. Computing the concurrence as a measure that determines to what extent the bipartite DNA-mRNA can be correlated through entanglement, is given. Preventing the entanglement loss is crucial for controlling unfavorable point mutations under environmental influences. We explore which physical parameters may affect the preservation of entanglement between DNA and mRNA pair systems, despite the destructive role of interaction with the environments.

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.

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.

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).

Chronobiology Meets Quantum Biology: A New Paradigm Overlooking the Horizon?

Biological processes and physiological functions in living beings are featured by oscillations with a period of about 24 h (circadian) or cycle at the second and third harmonic (ultradian) of the basic frequency, driven by the biological clock. This molecular mechanism, common to all kingdoms of life, comprising animals, plants, fungi, bacteria, and protists, represents an undoubted adaptive advantage allowing anticipation of predictable changes in the environmental niche or of the interior milieu. Biological rhythms are the field of study of Chronobiology. In the last decade, growing evidence hints that molecular platforms holding up non-trivial quantum phenomena, including entanglement, coherence, superposition and tunnelling, bona fide evolved in biosystems. Quantum effects have been mainly implicated in processes related to electromagnetic radiation in the spectrum of visible light and ultraviolet rays, such as photosynthesis, photoreception, magnetoreception, DNA mutation, and not light related such as mitochondrial respiration and enzymatic activity. Quantum effects in biological systems are the field of study of Quantum Biology. Rhythmic changes at the level of gene expression, as well as protein quantity and subcellular distribution, confer temporal features to the molecular platform hosting electrochemical processes and non-trivial quantum phenomena. Precisely, a huge amount of molecules plying scaffold to quantum effects show rhythmic level fluctuations and this biophysical model implies that timescales of biomolecular dynamics could impinge on quantum mechanics biofunctional role. The study of quantum phenomena in biological cycles proposes a profitable “entanglement” between the areas of interest of these seemingly distant scientific disciplines to enlighten functional roles for quantum effects in rhythmic biosystems.

Rotational Spectroscopy of 2-Furoic Acid and Its Dimer: Conformational Distribution and Double Proton Tunneling

Structural and tunneling properties of the 2-furoic acid (FA) monomer and dimer were investigated using rotational spectroscopy and DFT calculations. CREST, a conformational ensemble space exploration tool, was used to identify all possible low energy conformations of the FA monomer and dimer, followed by the DFT geometry optimization and harmonic frequency calculations. Broadband rotational spectra in the 2-6 GHz and in the 8-12 GHz regions were recorded in a supersonic jet expansion. The monomeric FA was found to exist dominantly as three different conformers: I , II , and III in a jet, with I and II taking on the trans -COOH configuration while III having the cis -COOH configuration. For the FA dimer, only the I - II conformer was observed experimentally, whereas the symmetric I - I and II - II conformers were not observed because of their zero dipole moments. The analysis of the splittings in the rotational transitions of I - II allowed one to extract the tunneling splitting to be 1056.0(12) MHz. The barrier height was determined to be ~442 cm -1 using the scaled potential energy scans at several different levels of theory.

Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities

To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.

Double Proton Transfer Across a Table: The Formic Acid Dimer-Fluorobenzene Complex

Proton transfer via tunneling is a fundamental quantum‐mechanical phenomenon. We report rotational spectroscopy measurements of this process in the complex of the formic acid dimer with fluorobenzene. The assignment of the spectrum indicates that this complex exists in the form of a π–π stacked structure. Each rotational transition of the parent isotopologue exhibits splitting. Isotopic substitution experiments show that the spectral splitting results from double‐proton transfer tunneling in the formic acid dimer. Presence of fluorobenzene as a neighboring molecule does not quench the double proton transfer in the formic acid dimer but decreases its tunneling splitting from 341(3) MHz to 267.608(1) MHz. Calculations suggest that the presence of the weakly bounded fluorobenzene does not influence the activation energy of the proton transfer. The fluorobenzene is reoriented with respect to the formic acid dimer during the course of the reaction, slowing down the proton transfer motion.

Mechanism of Side Chain-Controlled Proton Conductivity in Bioinspired Peptidic Nanostructures

Bioinspired peptide assemblies are promising candidates for use as proton-conducting materials in electrochemical devices and other advanced technologies. Progress toward applications requires establishing foundational structure-function relationships for transport in these materials. This experimental-theoretical study sheds light on how the molecular structure and proton conduction are linked in three synthetic cyclic peptide nanotube assemblies that comprise the three canonical basic amino acids (lysine, arginine, and histidine). Experiments find an order of magnitude higher proton conductivity for lysine-containing peptide assemblies compared to histidine and arginine containing assemblies. The simulations indicate that, upon peptide assembly, the basic amino acid side chains are close enough to enable direct proton transfer. The proton transfer kinetics is determined in the simulations to be governed by the structure and flexibility of the side chains. Together, experiments and theory indicate that the proton mobility is the main determinant of proton conductivity, critical for the performance of peptide-based devices.

Unitary structure of palindromes in DNA

We investigate the quantum behavior encountered in palindromes within DNA structure. In particular, we reveal the unitary structure of usual palindromic sequences found in genomic DNAs of all living organisms, using the Schwinger's approach. We clearly demonstrate the role played by palindromic configurations with special emphasis on physical symmetries, in particular subsymmetries of unitary structure. We unveil the prominence of unitary structure in palindromic sequences in the sense that vitally significant information endowed within DNA could be transformed unchangeably in the process of transcription. We introduce a new symmetry relation, namely purine-purine or pyrimidine-pyrimidine symmetries (p-symmetry) in addition to the already known symmetry relation of purine-pyrimidine symmetries (pp-symmetry) given by Chargaff's rule. Therefore, important vital functions of a living organisms are protected by means of these symmetric features. It is understood that higher order palindromic sequences could be generated in terms of the basis of the highest prime numbers that make up the palindrome sequence number. We propose that violation of this unitary structure of palindromic sequences by means of our proposed symmetries leads to a mutation in DNA, which could offer a new perspective in the scientific studies on the origin and cause of mutation.

A simplistic computational procedure for tunneling splittings caused by proton transfer

In this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.

Energy, Entropy and Quantum Tunneling of Protons and Electrons in Brain Mitochondria: Relation to Mitochondrial Impairment in Aging-Related Human Brain Diseases and Therapeutic Measures

Adult human brains consume a disproportionate amount of energy substrates (2-3% of body weight; 20-25% of total glucose and oxygen). Adenosine triphosphate (ATP) is a universal energy currency in brains and is produced by oxidative phosphorylation (OXPHOS) using ATP synthase, a nano-rotor powered by the proton gradient generated from proton-coupled electron transfer (PCET) in the multi-complex electron transport chain (ETC). ETC catalysis rates are reduced in brains from humans with neurodegenerative diseases (NDDs). Declines of ETC function in NDDs may result from combinations of nitrative stress (NS)-oxidative stress (OS) damage; mitochondrial and/or nuclear genomic mutations of ETC/OXPHOS genes; epigenetic modifications of ETC/OXPHOS genes; or defects in importation or assembly of ETC/OXPHOS proteins or complexes, respectively; or alterations in mitochondrial dynamics (fusion, fission, mitophagy). Substantial free energy is gained by direct O2-mediated oxidation of NADH. Traditional ETC mechanisms require separation between O2 and electrons flowing from NADH/FADH2 through the ETC. Quantum tunneling of electrons and much larger protons may facilitate this separation. Neuronal death may be viewed as a local increase in entropy requiring constant energy input to avoid. The ATP requirement of the brain may partially be used for avoidance of local entropy increase. Mitochondrial therapeutics seeks to correct deficiencies in ETC and OXPHOS.

A quantum mechanical approach to random X chromosome inactivation

<abstract> <p>The X chromosome inactivation is an essential mechanism in mammals' development, that despite having been investigated for 60 years, many questions about its choice process have yet to be fully answered. Therefore, a theoretical model was proposed here for the first time in an attempt to explain this puzzling phenomenon through a quantum mechanical approach. Based on previous data, this work theoretically demonstrates how a shared delocalized proton at a key base pair position could explain the random, instantaneous, and mutually exclusive nature of the choice process in X chromosome inactivation. The main purpose of this work is to contribute to a comprehensive understanding of the X inactivation mechanism with a model proposal that can complement the existent ones, along with introducing a quantum mechanical approach that could be applied to other cell differentiation mechanisms.</p> </abstract>

A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization

For the first time, at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory, a comprehensive quantum-mechanical investigation of the physico-chemical mechanism of the tautomeric wobblization of the four biologically-important G·C nucleobase pairs by the participation of the monomers in rare, in particular mutagenic, tautomeric forms (marked with an asterisk) was provided. These novel tautomeric transformations (wobblization or shifting of the bases within the pair) are intrinsically inherent properties of the G·C nucleobase pairs. In this study, we have obtained intriguing results, lying far beyond the existing representations. Thus, it was shown that Löwdin's G*·C*(WC) base pair does not tautomerize according to the wobblization mechanism. Tautomeric wobblization of the G*·C*(rWC) (relative Gibbs free energy ΔG = 0.00/relative electronic energy ΔE = 0.00 kcal·mol-1) ("r"-means the configuration of the base pair in reverse position; "WC"-the classic Watson-Crick configuration) and G*t·C*(H) (ΔG = -0.19/ΔE = 0.29 kcal·mol-1) ("H"-Hoogsteen configuration;"t" denotes the O6H hydroxyl group in the trans position) base pairs are preceded by the stages of the base pairs tautomerization by the single proton transfer (SPT). It was established that the G*t·C*(rH) (ΔG = 2.21/ΔE = 2.81 kcal·mol-1) base pair can be wobbled through two different pathways via the traditional one-stage mechanism through the TSs, which are tight G+·C- ion pairs, stabilized by the participation of only two intermolecular H-bonds. It was found out that the G·C base pair is most likely incorporated into the DNA/RNA double helix with parallel strands in the G*·C*(rWC), G·C*(rwwc), and G*·C(rwwc) ("w"-wobble configuration of the pair) tautomeric forms, which are in rapid tautomeric equilibrium with each other. It was proven that the G*·C*(rWC) nucleobase pair is also in rapid tautomeric equilibrium with the eight tautomeric forms of the so-called Levitt base pair. It was revealed that a few cases of tautomerization via the DPT of the nucleobase pairs by the participation of the C8H group of the guanine had occurred. The biological role of the obtained results was also made apparent.

A New Bias Site for Epigenetic Modifications: How Non-Canonical GC Base Pairs Favor Mechanochemical Cleavage of DNA

Properties of non-canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms involving of 5-methylcytosine, is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar-phosphate backbone of DNA after cytosines, the asymmetric character of these breaks, and an increase in break frequency in CpG after cytosine methylation. As an alternative hypothesis, probable implication of GC⁺ Hoogsteen base pairs is considered, which now exemplify the best-studied non-canonical GC base pairs in the DNA double helix. Also see the video abstract here https://youtu.be/EUunVWL0ptw.

Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations

The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core–hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.

Influence of local microenvironment on the double hydrogen transfer in porphycene

We performed time-resolved transient absorption and fluorescence anisotropy measurements in order to study tautomerization of porphycene in rigid polymer matrices at cryogenic temperatures. Studies were carried out in poly(methyl methacrylate) (PMMA), poly(vinyl butyral) (PVB), and poly(vinyl alcohol) (PVA). The results prove that in all studied media hydrogen tunnelling plays a significant role in the double hydrogen transfer which becomes very sensitive to properties of the environment below approx. 150 K. We also demonstrate that there exist two populations of porphycene molecules in rigid media: "hydrogen-transferring" molecules, in which tautomerization occurs on time scales below 1 ns and "frozen" molecules in which double hydrogen transfer is too slow to be monitored with nanosecond techniques. The number of "frozen" molecules increases when the sample is cooled. We explain this effect by interactions of guest molecules with a rigid host matrix which disturbs symmetry of porphycene and hinders tunnelling. Temperature dependence of the number of hydrogen-transferring molecules suggests that the factor which restores the symmetry of the double-minimum potential well in porphycene are intermolecular vibrations localized in separated regions of the amorphous polymer.

Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey

For the first time, in this study with the use of QM/QTAIM methods we have exhaustively investigated the tautomerization of the biologically-important conformers of the G*·C* DNA base pair-reverse Löwdin G*·C*(rWC), Hoogsteen G*'·C*(H), and reverse Hoogsteen G*'·C*(rH) DNA base pairs-via the single (SPT) or double (DPT) proton transfer along the neighboring intermolecular H-bonds. These tautomeric reactions finally lead to the formation of the novel G· C O 2 * (rWC), G N 2 * · C(rWC), G*'N2·C(rWC), G N 7 * · C(H), and G*'N7·C(rH) DNA base mispairs. Gibbs free energies of activation for these reactions are within the range 3.64-31.65 kcal·mol-1 in vacuum under normal conditions. All TSs are planar structures (Cs symmetry) with a single exception-the essentially non-planar transition state TSG*·C*(rWC)↔G+·C-(rWC) (C1 symmetry). Analysis of the kinetic parameters of the considered tautomerization reactions indicates that in reality only the reverse Hoogsteen G*'·C*(rH) base pair undergoes tautomerization. However, the population of its tautomerised state G*'N7·C(rH) amounts to an insignificant value-2.3·10-17. So, the G*·C*(rWC), G*'·C*(H), and G*'·C*(rH) base pairs possess a permanent tautomeric status, which does not depend on proton mobility along the neighboring H-bonds. The investigated tautomerization processes were analyzed in details by applying the author's unique methodology-sweeps of the main physical and chemical parameters along the intrinsic reaction coordinate (IRC). In general, the obtained data demonstrate the tautomeric mobility and diversity of the G*·C* DNA base pair.