Assessing the importance of proton transfer reactions in DNA

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.

Using dopants in the atmospheric pressure chemical ionization ion source to determine the site of protonation by ion mobility spectrometry

RATIONALE

Compounds like caffeine metabolites with more than one proton acceptor site can produce a mixture of isomeric protonated ions (protomers) in electrospray ionization and atmospheric pressure chemical ionization (APCI) ion sources. Discrimination between the protomers is of interest as the charge location influences ion structure and chemical and physical properties.

METHODS

Protonation of caffeine in an APCI ion source was studied using ion mobility spectrometry. The hydronium ions, H3O+(H2O)n, are the main reactant ions in the APCI ion source. Different dopant gases including NO2, NH3, and CH3NH2 were used to produce new reactant ions NO+, NH4 +, and CH3NH3 +, respectively. Density functional theory was employed to explain the experimental results and calculate the energies of the ionization reactions.

RESULTS

The ion mobility spectrum of caffeine showed three peaks. In the presence of NO2 dopant and NO+ reactant ion, caffeine was ionized via charge transfer and formation of M+ ion. As NH3 and CH3NH2 are stronger bases than H2O, the reactant ions NH4 + and CH3NH3 + selectively protonated the more basic site of caffeine, that is, the imidazole nitrogen. Using these dopants, we could attribute the first ion mobility peak to M+ ion, the second peak to the protonation of caffeine at the carbonyl oxygen atom, and the third peak to the protonation of the imidazole nitrogen atom. The calculated collisional cross-sections of M+ and the protomers of caffeine confirmed the peaks' assignment.

CONCLUSIONS

The criterion for the selection of an appropriate dopant is that its proton affinity (PA) should be between those of the proton acceptor sites of the molecule studied.

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.

Secondary ionization of pyrimidine nucleobases and their microhydrated derivatives in helium nanodroplets

Radiation damage in biological systems by ionizing radiation is predominantly caused by secondary processes such as charge and energy transfer leading to the breaking of bonds in DNA. Here, we study the fragmentation of cytosine (Cyt) and thymine (Thy) molecules, clusters and microhydrated derivatives induced by direct and indirect ionization initiated by extreme-ultraviolet (XUV) irradiation. Photofragmentation mass spectra and photoelectron spectra of free Cyt and Thy molecules are compared with mass and electron spectra of Cyt/Thy clusters and microhydrated Cyt/Thy molecules formed by aggregation in superfluid helium (He) nanodroplets. Penning ionization after resonant excitation of the He droplets is generally found to cause less fragmentation compared to direct photoionization and charge-transfer ionization after photoionization of the He droplets. When Cyt/Thy molecules and oligomers are complexed with water molecules, their fragmentation is efficiently suppressed. However, a similar suppression of fragmentation is observed when homogeneous Cyt/Thy clusters are formed in He nanodroplets, indicating a general trend. Penning ionization electron spectra (PIES) of Cyt/Thy are broad and nearly featureless but PIES of their microhydrated derivatives point at a sequential ionization process ending in unfragmented microsolvated Cyt/Thy cations.

Mechanism of formation and ion mobility separation of protomers and deprotomers of diaminobenzoic acids and aminophthalic acids

Aminobenzoic acids are well-established candidates for understanding the formation of isomeric ions in positive mode electrospray ionization as they yield both N- and O-protomers (prototropic isomers) at the amine and carbonyl sites, respectively. In the present work, a combination of ion mobility-mass spectrometry and density functional theory calculations to determine the protonation and deprotonation behaviour of four diamino benzoic acid and four aminophthalic acid isomers is presented. The additional COOH group on the ring of aminophthalic acids provides experimental evidence regarding the mechanism of intramolecular NH₃⁺ → O proton transfer, which has been the subject of debate in recent years. To determine the proton acceptor O atom, ion mobility spectra of the fragments of protomers were used as a new method for the confidential assignment of the O-protomer structure, confirming only short-distance intramolecular NH₃⁺ → O proton transfer. Additionally, the substitution pattern both influences the basicity of the protonation sites and enables these molecules to form internal hydrogen bonds with the protonated or deprotonated sites. The formation of the hydrogen bonds in the deprotonated aminophthalic acids changed the charge distribution and subsequently their ion mobility-derived collision cross sections in nitrogen (CCS_N2) leading to separation of the four isomers studied. Finally, an interesting effect of the substitution pattern was observed as a synergistic electron-donating effect of the amine groups of 3,5-diaminobenzoic acid on enhancing the basicity of the carbon atom C2 of the ring and previously unreported formation of a C-protomer within aminobenzoic acid systems.

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.

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.

Hydrogen migration in inner-shell ionized halogenated cyclic hydrocarbons

We have studied the fragmentation of the brominated cyclic hydrocarbons bromocyclo-propane, bromocyclo-butane, and bromocyclo-pentane upon Br(3d) and C(1s) inner-shell ionization using coincidence ion momentum imaging. We observe a substantial yield of CH₃⁺ fragments, whose formation requires intramolecular hydrogen (or proton) migration, that increases with molecular size, which contrasts with prior observations of hydrogen migration in linear hydrocarbon molecules. Furthermore, by inspecting the fragment ion momentum correlations of three-body fragmentation channels, we conclude that CH_x⁺ fragments (with x = 0, …, 3) with an increasing number of hydrogens are more likely to be produced via sequential fragmentation pathways. Overall trends in the molecular-size-dependence of the experimentally observed kinetic energy releases and fragment kinetic energies are explained with the help of classical Coulomb explosion simulations.

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.

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.

Improved proton-transfer barriers with van der Waals density functionals: Role of repulsive non-local correlation

Proton-transfer (PT) between organic complexes is a common and important biochemical process. Unfortunately, PT energy barriers are difficult to accurately predict using density functional theory (DFT); in particular, using the generalized gradient approximation (GGA) tends to underestimate PT barriers. Moreover, PT typically occurs in environments where dispersion forces contribute to the cohesion of the system; thus, a suitable exchange-correlation functional should accurately describe both dispersion forces and PT barriers. This paper provides benchmark results for the PT barriers of several density functionals including several variants of the van der Waals density functional (vdW-DF).The benchmark set comprises small organic molecules with inter- and intra-molecular PT. The results show that replacing GGA correlation with a fully non-local vdW-DF correlation increases the PT barriers, making it closer to the quantum chemical reference values.In contrast, including non-local correlations with the Vydrov-Voorhis (VV) method or dispersion-corrections at the DFT-D3 or the Tkatchenko-Scheffler (TS) levelhas barely any impact on the PT barriers.Hybrid functionals also increase and improve the energies,resulting in excellent performance of hybrid versions of the van der Waals density functionals vdW-DF-cx and vdW-DF2-B86R. For the formic acid dimer PT system, we analyzed the GGA exchange and non-local correlation contributions. The analysis shows that the repulsive part of the non-local correlation kernel plays a key role in the PT energy barriers predicted with vdW-DF.

Excited-State Intramolecular Proton Transfer in 2-(2'-Hydroxyphenyl)pyrimidines: Synthesis, Optical Properties, and Theoretical Studies

The development of fluorescence materials with switched on/off emission has attracted great attention owing to the potential application of these materials in chemical sensing. In this work, the photophysical properties of a series of original 2-(2'-hydroxyphenyl)pyrimidines were thoroughly studied. The compounds were prepared by following well-established and straightforward methodologies and showed very little or null photoluminescence both in solution and in the solid state. This absence of emission can be explained by a fast proton transfer from the OH group to the nitrogen atoms of the pyrimidine ring to yield an excited tautomer that deactivates through a nonradiative pathway. The key role of the OH group in the emission quenching was demonstrated by the preparation of 2'-unsubstituted derivatives, all of which exhibited violet or blue luminescence. Single crystals of some compounds suitable for an X-ray diffraction analysis could be obtained, which permitted us to investigate inter- and intramolecular interactions and molecular packing structures. The protonation of the pyrimidine ring by an addition of trifluoroacetic acid inhibited the excited-state intramolecular proton transfer (ESIPT) process, causing a reversible switch on fluorescence response detectable by the naked eye. This acidochromic behavior allows 2-(2'-hydroxyphenyl)pyrimidines to be used as solid-state acid-base vapor sensors and anticounterfeiting agents. Extensive density functional theory and its time-dependent counterpart calculations at the M06-2X/6-31+G** level of theory were performed to rationalize all the experimental results and understand the impact of protonation on the different optical transitions.

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

A detailed kinetic study on the tautomerization reactions of barbituric acid: A combined DFT-QTAIM analysis

A detailed kinetic study on the tautomerization reactions of barbituric acid (BA) at elevated temperatures from 270 K up to 1000 K was performed in this work. The B3LYP/6-311 + G(3df,2p) density functional theory (DFT) calculations were performed to evaluate the rate constants of transition states (TS) conversions of the tautomerization reactions. The connections from a given TS to the corresponding local minima of the reactant and product sides were confirmed by means of employing the intrinsic reaction coordinate (IRC) method. Moreover, the quantum theory of atoms in molecules (QTAIM) approach was employed to analyze the molecular mechanisms of reactions. The effects of vibrational normal mode frequencies of the reactant and TS were investigated on the curvature of the corresponding Arrhenius plot in the presence and absence of the tunneling effect. For each tautomerization reaction, the investigated reaction was partitioned into three different stages and four zones. The obtained results were plotted along with the corresponding reaction coordinates for each reaction considering and comparing different factors in agreement with already affirmed concepts. As a consequence, details of performed kinetic study on the tautomerization reactions of BA were successfully provided in this work.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Elaborating the excited-state double proton transfer mechanism and multiple fluorescent characteristics of 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole

Recently, Krishnamoorthy and coworkers reported a new type of proton transfer, which was labeled as 'proton transfer triggered proton transfer', in 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole (bis-HPTA). In this work, the excited-state double proton transfer (ESDPT) mechanism and multiple fluorescent characteristics of bis-HPTA were investigated. Upon photo-excitation, the intramolecular hydrogen bonding strength changed and the electron density of bis-HPTA redistributed. These changes will affect the proton transfer process. In S₀ state, the proton transfer processes of bis-HPTA were prohibited on the stepwise and concerted pathways. After vertical excitation to the S₁ state, the ESIPT-II process was more likely to occur than the ESIPT-I process, which was contrary to the conclusion that the ESIPT-II process is blocked and the ESIPT-II process takes place after the ESIPT-I process proposed by Krishnamoorthy and coworkers. When the K2 tautomer was formed through the ESIPT-II process, the second proton transfer process on the stepwise pathway was prohibited. On another stepwise pathway, after the ESIPT-I process (form the K1 tautomer), the second proton transfer process should overcome a higher potential barrier than the ESIPT-I process to form ESDPT tautomer. On the concerted pathway, the bis-HPTA can synchronous transfer double protons to form the ESDPT tautomer. The ESDPT tautomer was unstable and immediately converted to the K2 tautomer via a barrierless reverse proton transfer process. Thus, the fluorescent maximum at 465 nm from the ESDPT tautomer reported by Krishnamoorthy and coworkers was ascribed to the K2 tautomer. Most of the fluorophores show dual fluorescent properties, while the bis-HPTA undergoing ESDPT process exhibited three well-separated fluorescent peaks, corresponding to its normal form (438 nm), K1 tautomer (462 nm) and K2 tautomer (450 nm), respectively.

Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation

The pK_a values of reactive protons in 8-oxoG˙⁺ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.

Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media

Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.

The influence of base pair tautomerism on single point mutations in aqueous DNA

The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.

Heavy N+ ion transfer in doubly charged N2Ar van der Waals cluster

Van der Waals clusters are weakly bound atomic/molecular systems and are an important medium for understanding micro-environmental chemical phenomena in bio-systems. The presence of neighboring atoms may open channels otherwise forbidden in isolated atoms/molecules. In hydrogen-bond clusters, proton transfer plays a crucial role, which involves mass and charge migration over large distances within the cluster and results in its fragmentation. Here we report an exotic transfer channel involving a heavy N⁺ ion observed in a doubly charged cluster produced by 1 MeV Ne⁸⁺ ions: (N₂Ar)²⁺→N⁺+NAr⁺. The neighboring Ar atom decreases the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{N}}_2^{2 + }$$\end{document}N22+ barrier height and width, resulting in significant shorter lifetimes of the metastable molecular ion state \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{N}}_2^{2 + }$$\end{document}N22+(\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${{\mathrm{X}}^{1}}{\Sigma _{{\mathrm{g}}}^{+}}$$\end{document}X1Σg+). Consequently, the breakup of the covalent N⁺−N⁺ bond, the tunneling out of the N⁺ ion from the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{N}}_2^{2 + }$$\end{document}N22+ potential well, as well as the formation of an N−Ar⁺ bound system take place almost simultaneously, resulting in a Coulomb explosion of N⁺ and NAr⁺ ion pairs.

There are multiple ways by which energy and charge transfer occur in weakly bound systems. Here the authors reveal a heavy ion N⁺ transfer in a doubly charged Van der Waals cluster produced in collisions of the highly charged Ne⁸⁺ ion with N₂Ar, leading to fragmentation of N⁺ and NAr⁺ via Coulomb explosion.

Tautomers of homophthalic anhydride in the ground and excited electronic states: analysis through energy, hardness and vibrational signatures

The keto-enol tautomerisation in homophthalic anhydride (HA) is investigated in the ground (S₀) and excited (S₁) electronic states. The keto form with a dicarbonyl structure is found to be the most stable form in S₀ and enol form with a monocarbonyl structure in S₁ indicating an excited state intramolecular proton transfer (ESIPT) process. The computed results show consistency with the change in basis sets and methods of calculations. Apart from the two tautomers, transition states are also identified. The barrier to interconversion is found to reduce substantially in S₁. Internal reaction coordinate (IRC) calculations confirm the pathway of interconversion between the two forms in S₀ and S₁. The observed FT-IR spectra corroborate well with our computed spectra. The appearance of two strong lines around 1800 cm^-1 confirms the lowest energy structure to be the keto tautomer with a dicarbonyl form in S₀. Our computations corroborate well with the crystal structure data for an analogous molecule. Electron distribution in HOMO and LUMO indicate the excitation process as π → π^* in nature. The qualitative chemical concepts like hardness and electrophilicity are calculated to estimate the stability of the tautomers. The energy and hardness profiles with the variation of IRC are opposite to each other, verifying the principle of maximum hardness.

Proton Transfer vs Complex Formation Channels in Ionized Formic Acid Dimer: A Direct Ab Initio Molecular Dynamics Study

Photoirradiation to a hydrogen-bonded system plays an important role in the initial DNA and enzyme damage processes. The formic acid (FA) dimer is a model compound of double proton transfer systems, such as DNA base pairs. In the present study, the reactions of the FA dimer cation, formed upon ionization of the neutral dimer, have been investigated by the direct ab initio molecular dynamics method. Two reaction channels were identified for the FA dimer cation: complex formation and proton transfer (PT). In the complex formation channel, the carbonyl oxygen atoms of the two FA monomers were bound symmetrically, and a face-to-face complex was formed. In the PT channel, the proton of FA⁺ was transferred to FA, forming the H⁺(HCOOH)--HCO₂ radical cation as product. At low temperature, the complex channel was dominant, whereas the PT channel increased with increasing temperature. The asymmetric spin distribution on the FA dimer cation exhibited a strong correlation with the PT channel.

Bend-to-Break: Curvilinear Proton Transfer in Phenol-Ammonia Clusters

The electric field experienced by the OH group of phenol embedded in the cluster of ammonia molecules depends on the relative orientation of the ammonia molecules, and a critical field of 236 MV cm^-1 is essential for the transfer of a proton from phenol to the surrounding ammonia cluster. However, exceptions to this rule were observed, which indicates that the projection of the solvent electric field over the O-H bond is not a definite descriptor of the proton transfer reaction. Therefore, a critical electric field is necessary, but it is not a sufficient condition for the proton abstraction. This, in combination with an adequate solvation of the acceptor ammonia molecule in a triple donor motif that energetically favors the proton transfer process, constitutes necessary and sufficient conditions for the spontaneous proton abstraction. The proton transfer process in phenol-(ammonia)_n clusters is statistically favored to occur away from the plane of the phenyl ring and follows a curvilinear path which includes the O-H bond elongation and out-of-plane movement of the proton. Colloquially, this proton transfer can be referred to as a "bend-to-break" process.

Tuning the excited-state intramolecular proton transfer (ESIPT) process of indole–pyrrole systems by π-conjugation and substitution effects: experimental and computational studies

A series of amino (NH)-type hydrogen-bonding (H-bonding) compounds, BNDAB-1–4, containing π-enlarged indole and β-ethoxycarbonyl-substituted pyrrole units were designed and synthesized.

Electron and hole interactions with P, Z, and P:Z and the formation of mutagenic products by proton transfer reactions

Z would act as an electron acceptor and P would capture a hole in the unnatural DNA. The latter process would produce mutagenic products via a proton transfer reaction.

Double Proton Transfer in the Dimer of Formic Acid: An Efficient Quantum Mechanical Scheme

Double proton transfer plays an important role in biology and chemistry, such as with DNA base pairs, proteins and molecular clusters, and direct information about these processes can be obtained from tunneling splittings. Carboxylic acid dimers are prototypes for multiple proton transfer, of which the formic acid dimer is the simplest one. Here, we present efficient quantum dynamics calculations of ground-state and fundamental excitation tunneling splittings in the formic acid dimer and its deuterium isotopologues. These are achieved with a multidimensional scheme developed by us, in which the saddle-point normal coordinates are chosen, the basis functions are customized for the proton transfer process, and the preconditioned inexact spectral transform method is used to solve the resultant eigenvalue problem. Our computational results are in excellent agreement with the most recent experiments (Zhang et al., 2017; Li et al., 2019).

Probing interaction of a trilysine peptide with DNA underlying formation of guanine-lysine cross-links: insights from molecular dynamics

DNA-protein cross-links constitute bulky DNA lesions that interfere with the cellular machinery. Amongst these stable covalently tethered adducts, the efficient nucleophilic addition of the free amino group of lysines onto the guanine radical cation has been evidenced. In vitro addition of a trilysine peptide onto a guanine radical cation generated in a TGT oligonucleotide is so efficient that competitive addition of a water molecule, giving rise to 8-oxo-7,8-dihydroguanine, is not observed. This suggests a spatial proximity between guanine and lysine for the stabilization of the prereactive complex. We report all-atom microsecond scale molecular dynamics simulations that probe the structure and interactions of the trilysine peptide (KKK) with two oligonucleotides. Our simulations reveal a strong, electrostatically driven yet dynamic interaction, spanning several association modes. Furthermore, the presence of neighbouring cytosines has been identified as a factor favoring KKK binding. Relying on ab initio molecular dynamics on a model system constituted of guanine and methylammonium, we also corroborate a mechanistic pathway involving fast deprotonation of the guanine radical cation followed by hydrogen transfer from ammonium leaving as a result a nitrogen reactive species that can subsequently cross-link with guanine. Our study sheds new light on a ubiquitous mechanism for DNA-protein cross-links also stressing out possible sequence dependences.

The Role of Proton Transfer on Mutations

Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.

Modeling the action of environment on proton tunneling in the adenine-thymine base pair

Effect of environment coupling on the quantum-biological phenomenon of proton tunneling in the hydrogen bonds of the adenine-thymine base pair in DNA was modeled within the framework of quantum statistics and perturbation theory. A number of important thermodynamic indicators including partition function, free energy, and entropy were then calculated and examined. The proton was then assumed to be subject to an attraction represented by a double-well potential energy surface with a small asymmetry, which was considered as the perturbation introduced to the system. The action of environment manifested itself in the form of a global minimum in the free energy curve, as an implicit implication of the tendency of the system toward randomness and disorder, at which no spontaneous change such as quantum tunneling will accordingly occur. Furthermore, assuming the free energy to be in a close neighborhood of its minimum truly explained the smallness of the contribution of environment coupling to the tunneling probability reported in the literature based on the fact that the closer the free energy to its minimum, the less the transition probability to this point.

Unraveling the Mechanisms of the Excited-State Intermolecular Proton Transfer (ESPT) for a D-π-A Molecular Architecture

Precise revealing the mechanisms of excited-state intermolecular proton transfer (ESPT) and the corresponding geometrical relaxation upon photoexcitation and photoionization remains a formidable challenge. In this work, the compound (E)-4-(((4H-1,2,4-triazol-4-yl)imino)methyl)-2,6-dimethoxyphenol (TIMDP) adopting a D-π-A molecular architecture featuring a significant intramolecular charge transfer (ICT) effect has been designed. With the presence of perchloric acid (35 %), TIMDP can be dissolved through the formation of a HClO₄ -H₂ O-OH(TIMDP)-N(TIMDP) hydrogen-bonding bridge. At the ground state, the ICT effect is dominant, giving birth to crystals of TIMDP. Upon external stimuli (e.g., UV light irradiation, electro field), the excited state is achieved, which weakens the ICT effect, and significantly promotes the ESPT effect along the hydrogen-bonding bridge, resulting in crystals of [HTIMDP]⁺ ⋅[H₂ O]⋅[ClO₄ ]^- . As a consequence, the mechanisms of the ESPT can be investigated, which distorted the D-π-A molecular architecture, tuned the emission color with the largest Stokes shift of 242 nm, and finally, high photoluminescence quantum yields (12 %) and long fluorescence lifetimes (8.6 μs) have achieved. These results not only provide new insight into ESPT mechanisms, but also open a new avenue for the design of efficient ESPT emitters.

Effect of Basicity and Structure on the Hydration of Protonated Molecules, Proton-Bound Dimer and Cluster Formation: An Ion Mobility-Time of Flight Mass Spectrometry and Theoretical Study

Protonation, hydration, and cluster formation of ammonia, formaldehyde, formic acid, acetone, butanone, 2-ocatanone, 2-nonanone, acetophenone, ethanol, pyridine, and its derivatives were studied by IMS-TOFMS technique equipped with a corona discharge ion source. It was found that tendency of the protonated molecules, MH⁺, to participate in hydration or cluster formation depends on the basicity of M. The molecules with higher basicity were hydrated less than those with lower basicity. The mass spectra of the low basic molecules such as formaldehyde exhibited larger clusters of M_nH⁺(H₂O)_n, while for compounds with high basicity such as pyridine, only MH⁺ and MH⁺M peaks were observed. The results of DFT calculations show that enthalpies of hydrations and cluster formation decrease as basicities of the molecules increases. Using comparison of mass spectra of formic acid, formaldehyde, and ethanol, effect of structure on the cluster formation was also investigated. Formation of symmetric (MH⁺M) and asymmetric proton-bound dimers (MH⁺N) was studied by ion mobility and mass spectrometry techniques. Both theoretical and experimental results show that asymmetric dimers are formed more easily between molecules (M and N) with comparable basicity. As the basicity difference between M and N increases, the enthalpy of MH⁺N formation decreases.

Theoretical Study of Adenine to Guanine Transition Assisted by Water and Formic Acid Using Steered Molecular Dynamic Simulations

The free energy profile of the adenine to guanine transition in the gas and aqueous phases was obtained by applying steered molecular dynamic (SMD) simulations. Three processes were considered to explain the mechanism assisted by water and formic acid molecules. The first process is hydrolytic deamination of adenine, then oxidation of the hypoxanthine previously formed, and finally, the animation from xanthine to guanine. In the gas phase these processes indicate a slow and not spontaneous conversion (ΔG g = 4.07 kcal·mol-1, k = 5.59·10-40 s-1), and a lifetime for guanine of τ = 7.75·10+22 s. The presence of solvent makes the transition more difficult by increasing the reaction energy to 26.90 kcal·mol-1 and decreasing the speed of the process to 1.63·10-55 s-1. However, it decreases the energy of the deamination process to -9.63 kcal·mol-1 and the lifetime of guanine base to τ = 6.85·10+17 s when the surrounding medium used in the transition process is aqueous. The results show that the guanine could participate in genetic mutations based on the lifetimes obtained. Transition states and intermediates structures were analyzed at the molecular dynamic level. This allows to follow the mechanism over time and to calculate thermodynamic and kinetic properties.

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.

Extended Efficacy of Low-Dose Valganciclovir for Prevention of Cytomegalovirus Disease in Intermediate-Risk Kidney Transplant Recipients: Two-Year Follow-Up

OBJECTIVES

In a previous study, we evaluated 1-year outcomes of using low-dose valganciclovir prophylaxis for cytomegalovirus infection in intermediate-risk kidney transplant recipients. Whether this effect persists in the long term is unknown. We aimed to evaluate the 2-year follow up of such adopted prophylaxis.

MATERIALS AND METHODS

We randomized 2 matched groups of kidney transplant recipients (1:1) to receive valganciclovir as 450 mg daily (group 1) or 900 mg daily (group 2) for the first 6 months after kidney transplant. The final analysis included 196 patients as intermediate-risk patients (98 in each treatment group) after exclusion of 5 high-risk patients. Serologically, all patients were at moderate risk for cytomegalovirus infection. Long-term outcomes including cytomegalovirus disease, acute rejection, new-onset diabetes after transplant, graft loss, and patient survival were assessed.

RESULTS

Through year 2 of follow-up, cytomegalovirus infection was reported in only 1 patient in group 1 (at month 13) and 1 patient in group 2 (at month 19) (not significant). Biopsy-proven acute rejection episodes were not statistically different between the groups (2 episodes in group 1 and 6 in group 2; P = .431). New-onset diabetes posttransplant was reported in 8.1% in group 1 and 13.2% in group 2 (P = .535). Graft failure was equal in both groups (1 in each group) at 2 years of follow up (not significant). Patient survival was comparable in both groups (100% in group 1 versus 97.9% in group 2; P = .661). The total number of cytomegalovirus infections at 2 years was numerically less in group 1 (P = .128).

CONCLUSIONS

Low-dose valganciclovir prophylaxis for 6 months was associated with sustained reduction of cytomegalovirus infection up to 2 years after kidney transplant without significant impact on the acute rejection, new-onset diabetes posttransplant, or patient and graft outcomes.