Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair

A rotational spectroscopy study of microsolvation effects on intramolecular proton transfer in trifluoroacetylacetone-(H2O)1-3

Trifluoroacetylacetone (TFAA) has two enol forms, which can switch to each other via proton transfer. While much attention has been paid to their conformational preferences, the influence of microsolvation on regulating the proton position remains unexplored. Herein, we report the rotational spectra of trifluoroacetylacetone-(water)n (n = 1-3) investigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency range. Two conformers were identified for both TFAA-H2O and TFAA-(H2O)2, while only one conformer was characterized for TFAA-(H2O)3. The results indicate that water binding on the CH3 side stabilizes the enolF form, whereas water binding on the CF3 side stabilizes the enolH form. The enolF form predominates over the enolH form in these hydrated complexes, which contrasts with the fact that only enolH exists in isolated TFAA. EnolH becomes preferred only when water inserts itself into the intramolecular hydrogen bond. Instanton theory calculations reveal that the proton transfer reaction is dominated by quantum tunneling at low temperatures, leading to the stable existence of only one enol form in each configuration of the hydrated clusters.

Computational analysis of anti-cancer drug hydroxyurea adsorption on nanocages of gold, silver and copper: SERS and DFT assessment

The use of nanostructures in targeted drug delivery is effective in decreasing anticancer drug toxicity. Here, we discuss the theoretically predicted adsorption and interaction behavior of hydroxyurea [HU] with nano metal cages (nmC). HU interact the nmC through the N4 in primary amine with energies of -29.776, -30.684 and -22.105 kcal/mol for Au, Ag and Cu cage, respectively. As a result of reactivity studies, HU complexes with nmC (Au/Ag/Cu) are becoming more electrophilic and this gives the nmC system their bioactivity. It is suggested that nanocage is going to change the FMO's energy levels by means of absorption, so that it is used in drug administration. DOS and MEP were accomplished to gain additional understandings into the reactivity of proposed complexes. Method for improving the Raman signal of biomolecules is surface enhanced Raman scattering (SERS), which uses nanosized metal substrates. Chemical enhancement is evidenced by Mulliken charge distributions of all systems for detection and chemical compositions and exerts a significant role in determining them. In HU complexes containing nmC (Au/Ag/Cu), electron density was detected via ELF and LOL calculations. Based on the results of a non-covalent interaction (NCI) analysis, Van der Waals/hydrogen bonds/repulsive steric - interactions have been found. The title compound will also be analyzed in order to determine its bioactivity and drug likeness parameters, as a result, we will able to create a molecule with a highly favorable pharmacological profile and use the docking method to determine the values of the interaction energies for drug delivery. This study suggests that adsorption of drugs on nanocage surface occurs physically and functionalizing the nanocage has increased adsorption energy.

Proton-polarized states in DNA

We observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions.

Non-covalent interaction, adsorption characteristics and solvent effect of procainamide anti-arrhythmias drug on silver and gold loaded silica surfaces: SERS spectroscopy, density functional theory and molecular docking investigations†

First-principle calculations were systematically carried out to explore the structural and electronic properties of the non-covalent interaction of procainamide (PA) anti-arrhythmias drug molecules on silver-loaded and gold-loaded silica nanostructures. Computed adsorption energies presented a higher affinity of PA towards the Ag–SiO₂ as compared with Au–SiO₂ surfaces. The non-covalent interaction analysis revealed a weak van der Waals type of forces and hydrogen bonding, associated with a noticeable repulsive steric interaction. It was conceived that silver and gold decorated silica can be used for drug administration in biological systems due to the fact that their frontier molecular orbital energy levels were considerably altered upon absorption, decreasing the pertinent energy gaps. Moreover, the electronic spectra of PA⋯Ag–SiO₂ and PA⋯Au–SiO₂ structures investigated in different solvents display a notable blue shift, suggesting that noble metal-loaded silica can be effective in the context of drug delivery systems. Therefore, silver- and gold-decorated silica of three possible drug adsorption scenarios was fully analyzed to realize the associated bioactivity and drug likeness. Theoretical findings suggest that Ag- and Au–SiO₂ nanocomposites can be considered potential drug delivery platforms for procainamide in medication protocols.

The structural and electronic properties of the non-covalent interaction of procainamide (PA) anti-arrhythmias drug molecules on silver-loaded and gold-loaded silica nanostructures were explored using first-principle calculations.

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.

Non-poissonian Distribution of Point Mutations in DNA

In general, for chemical reactions occurring in systems, where fluctuations are not negligibly small, it is necessary to introduce a master equation for distribution of probability of fluctuations. It has been established that the monomolecular reactions of a type as A ↔ X are described by the master equation, which leads to a Poisson distribution with the variance equal to the average value N 0. However, the consideration of the Löwdin mechanism as autocatalytic non-linear chemical reactions such as A + X ↔ 2X and the corresponding master equation lead to a non-Poissonian probability distribution of fluctuations. In the presented work, first-order autocatalysis has been applied to the Löwdin's mechanism of spontaneous mutations in DNA. Describing double proton transfers between complimentary nucleotide bases along the chain by first-order autocatalytic reactions, the corresponding master equation for protons in tautomeric states becomes non-linear, and at non-equilibrium conditions this leads to the non-Poissonian distribution of spontaneous mutations in DNA. It is also suggested that the accumulation of large fluctuations of successive cooperative concerted protons along the chain may produce higher non-linearities which could have a significant impact on some biochemical processes, occurring in DNA.

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.

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.

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.

Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation

In this paper we have theoretically predicted a novel pathway for the mutagenic tautomerization of the classical A∙T DNA base pairs in the free state, the Watson-Crick A·Т(WC), reverse Watson-Crick A·Т(rWC), Hoogsteen A·Т(H) and reverse Hoogsteen A·Т(rH) pairs, via sequential proton transfer accompanied by a significant change in the mutual orientation of the bases. Quantum-mechanical (QM) calculations were performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level in vacuum phase, along with Bader's quantum theory of Atoms in Molecules (QTAIM). These processes involve transition states (TSs) with quasi-orthogonal structures (symmetry C1), which are highly polar, tight ion pairs (A-, N6H2-deprotonated)∙(T+, O4/O2-protonated). Gibbs free energies of activation for the A∙T(WC) / A∙T(rWC) ↔ A*∙Т(rwWC) / A*∙Т(wWC) tautomeric transitions (~43.5 kcal∙mol-1) are lower than for the A∙T(H) / A∙T(rH) ↔ A*N7∙Т(rwH) / A*N7∙Т(wH) tautomerisations (~53.0 kcal∙mol-1) (rare tautomers are marked by an asterisk; w-wobble configured tautomerisation products). The (T)N3+H⋯N1-(A), (T)O4+H⋯N1-(A) / (T)N3+H⋯N1-(A) and (T)O2+H⋯N1-(A) H-bonds are found in the transition states TSA-·T+A·T(WC)↔A*·T(rwWC) / TSA-·T+A·T(rWC)↔A*·T(wWC). However, in the transition state TSA-·T+A·Т(H)↔A*N7·T(rwH) / TSA-·T+A·Т(rH)↔A*N7·T(wH), the (T)N3+H⋯N7-(A), (T)O4+H⋯N7-(A) / (T)N3+H⋯N7-(A) and (T)O2+H⋯N7-(A) H-bonds are supplemented by the attractive (T)O4+/O2+⋯N6-(A) van der Waals contacts. It was demonstrated that the products of the tautomerization of the classical A∙T DNA base pairs-A*∙Т(rwWC), A*N7∙Т(rwH) and A*N7∙Т(wH) (symmetry Cs)-further transform via double proton transfer into the energetically favorable wobble A∙T*(rwWC), A∙T*(rwH) and A∙T*O2(wH) base mispairs (symmetry Cs).

Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study

Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations. Two pathways were considered to explain the mechanism of this process, where the water molecule attacks the C–N bond to give an intermediate (an amino–hydroxy–oxo structure in the A-path, and a hydroxy–oxo in the B-path) as the determinant step of reaction. Stationary structures along both energy profiles were analyzed at molecular dynamics level, obtaining states with higher free energies than those from electronic calculations in the gas phase and in solution described as a continuous medium. From the results obtained, the more complex A-pathway, with five steps, was kinetically the most favorable (with an endergonic reaction energy of 7.41 kcal mol⁻¹, a high barrier of 67.53 kcal mol⁻¹, and a small velocity constant k₂ = 1.80 × 10⁻³⁷ s⁻¹), concluding that the uracil base can participate in a spontaneous genetic mutation since the uracil–ammonia complex has a long lifetime of 6.10 × 10²⁷ s. This process turns out exergonic and faster when carried out in gas phase simulation or electronic calculation with a continuous medium, due to the disappearance of explicit water molecules that can compete with the assistant molecule.

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwWC)/A·T*(wH)/A·T*(rwH) mutagenic tautomerization via sequential proton transfer: a QM/QTAIM study

In this study for the first time we have revealed by QM and QTAIM calculations at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory the novel routes of the mutagenic tautomerization of three biologically important A·T DNA base pairs – reverse Watson–Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) – followed by their rebuilding into the wobble (w) A·T*(rw_WC), A·T*(w_H) and A·T*(rw_H) base mispairs by the participation of the mutagenic tautomers of the DNA bases (denoted by asterisk) and vice versa, thus complementing the physico-chemical property of the canonical A·T(WC) Watson–Crick DNA base pair reported earlier (Brovarets' et al., RSC Adv., 2015, 5, 99594–99605). These non-dissociative tautomeric transformations in the classical A·T(rWC), A·T(H) and A·T(rH) DNA base pairs proceed similarly to the canonical A·T(WC) DNA base pair via the intrapair sequential proton transfer with shifting towards major or minor grooves of DNA followed by further double proton transfer along the intermolecular H-bonds and are controlled by the plane symmetric and highly stable transition states – tight ion pairs formed by the A⁺ nucleobase, protonated by the N1/N7 nitrogen atoms, and T⁻ nucleobase, deprotonated by the N3H imino group. Comparison of the estimated populations of the tautomerised states (10⁻²¹ to 10⁻¹⁴) with similar characteristics for the canonical A·T(WC) DNA base pair (10⁻⁸ to 10⁻⁷) leads authors to the conclusion, that only a base pair with WC architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development. Among all four classical DNA base pairs, only A·T(WC) DNA base pair can ensure the proper rate of the spontaneous point errors of replication in DNA.

We discovered tautomeric wobbling of the classical A·T DNA base pairs. This data evidence, that only a base pair with Watson–Crick architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development.

Tautomeric equilibria of isoguanine and related purine analogs

Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th "letters" in DNA.

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach

We have applied the systematic molecular fragmentation by annihilation (SMFA) fragmentation technique to glycine and DNA base pairs in water clusters, systems for which explicit solvation is believed to be important. The SMFA method was found to be capable of describing the structures, especially in handling the complexity of hydrogen bonding, with energies produced being comparable with those from full molecule results. Thus, the ability to break down large calculations into a manageable time without loss of accuracy shows promise for application to real biological systems for which these effects are relevant.

Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors

We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.

The nonadditivity of stacking interactions in adenine–thymine and guanine–cytosine stacked structures: Study by MP2 and SCS-MP2 calculations

The nonadditivity of stacking interactions in stacked structures of adenine–thymine and guanine–cytosine base pairs is investigated by MP2 and SCS-MP2 calculations with 6-311++G** and aug-cc-pvdz basis sets. The calculation results indicate that the intermolecular distances in the multi-stacked structures do not become shorter obviously as the stacked structure added. The middle stacking interaction energies in the multi-stacked structures also become weaker than that of dimer structures. It is found that the total stacking interaction energies of the trimer and tetramer stacked structures do not increase proportionally. Based on the results, we suggest that there is negative cooperativity of the stacking interactions in the adenine–thymine and guanine–cytosine stacked structures.

Possible use of BN-modified fullerene as a nano-biosensor to detect adenine–thymine Watson–Crick base pair in mutagenic tautomeric form: Theoretical approach

The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu 2+ cation and their interactions with BN doped fullerene ( C 58 BN ). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu 2+ complexes.

DNA spontaneous mutation and its role in the evolution of GC-content: assessing the impact of the genetic sequence

We use theoretical tools to investigate the possible role played by a DNA sequence in the base pair tautomerization phenomena.

Assessing the importance of proton transfer reactions in DNA

Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.

DPT tautomerisation of the wobble guanine·thymine DNA base mispair is not mutagenic: QM and QTAIM arguments

We have shown for the first time, connecting QM methods with QTAIM analysis and using the methodology of the sweeps of the energetical, electron-topological and geometrical parameters, that the tautomerisation of the wobble guanine·thymine (wG·T) DNA base mispair into the wG(*)·T(*) base mispair induced by the double proton transfer (DPT), which undergoes a concerted asynchronous pathway, is not mutagenic. The wG·T → wG(*)·T(*) DPT tautomerisation does not result in the transition of the G base into its mutagenic tautomeric form G(*) able to mispair with the T base within the Watson-Crick base pairing scheme. This observation is explained by the so-called quantum protection of the wG·T DNA base mispair from its mutagenic tautomerisation - the dynamical non-stability of the tautomerised wG(*)·T(*) base mispair and significantly negative value of the Gibbs free energy of activation for the reverse reaction of the wG·T → wG(*)·T(*) DPT tautomerisation.

Substrate dependent reaction channels of the Wolff-Kishner reduction reaction: A theoretical study

Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p) SCRF=(PCM, solvent = 1,2-ethanediol) optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H₂N–NH₂) and (H₂O)₈. A ready reaction channel of acetone → acetone hydrazine (Me₂C=N–NH₂) was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N₂ extrusion step from the isopropyl diimine intermediate (Me₂C(H)–N=N–H). Two base-catalyzed reactions were investigated by models of the ketone, H₂N–NH₂ and OH⁻(H₂O)₇. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N₂ extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenyl)ethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.

Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form.

Adsorption behavior of 6-Mercaptonicotinic acid on self-assembled gold nano-substrates explored by SERS combined with theoretical calculations

As a typical Raman reporter molecule, 6-Mercaptonicotinic acid (C6H5NO2S, MNA) has three atoms (i.e., N, O, and S), which could be potential to chemically interact with gold nano-surface. In the present report, the adsorption behavior of MNA on self-assembled gold nano-substrates is explored by means of surface-enhanced Raman scattering and theoretical calculations. The results reveal that all the enhanced bands are assigned to in-plane vibrations. The ring triangle breathing coupling with CS stretching band at 1108cm(-)(1) is enhanced a lot and redshifts to 1088cm(-)(1) in the SERS spectra. Furthermore, most of the bands related to N atom are apparently enhanced and shift in the SERS spectra. Based on the surface selection rule, it infers that MNA is vertically chemisorbed on self-assembled gold substrates through the S and the N atoms. The spectroscopic results are further interpreted by the density functional theory (DFT) calculations.

Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion

The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.

Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases

Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.