Effects of Intense Electric Fields on the Double Proton Transfer in the Watson–Crick Guanine–Cytosine Base Pair

How to search for and reveal a hidden intermediate? The ELF topological description of non-synchronicity in double proton transfer reactions under oriented external electric field

CONTEXT

The nature of double intermolecular proton transfer was studied with the ELF topological approach in two model dimers (the formic acid homodimer and the 1,2,3-triazole-guanidine heterodimer) under an oriented external electric field. It has been shown that each of the two dimers can have either a one-step (one transition state structure) or two-step (two transition state structures) reaction path, depending on the intensity and orientation of the external electric field. The presence of a singularly broad shoulder (plateau in the case of homodimer and plateau-like for heterodimer) around the formal transition state structure results from the strong asynchronicity of the reaction. A careful ELF topological analysis of the nature of protons, hydride (localized) or roaming (delocalized) proton, along the reaction path allowed us to unambiguously classify the one-step mechanisms governing the double-proton transfer reactions into three distinct classes: (1) concerted-synchronous, when two events (roaming proton regions) completely overlap, (2) concerted-asynchronous, when two events (roaming proton regions) partially overlap, and (3) two-stage one-step non-concerted, when two roaming proton regions are separated by a "hidden intermediate region". All the structures belonging to this separatrix region are of the zwitterion form.

METHODS

Geometry optimization of the stationary points on the potential energy surface was performed using density functional theory-wB97XD functional-in combination with the 6-311+ +G(2d, 2p) basis set for all the atoms. All first-principles calculations were performed using the Gaussian 09 quantum chemical packages. We also used the electron localization function (ELF) to reveal the nature of the proton along the reaction path: a bound proton (hydride) becomes a roaming proton (carrying a tiny negative charge ≈ 0.3 e) exchanging with two adjacent atoms via two attractors (topological critical points with (3, - 3) signature). The ELF analyses were performed using the TopMod package.

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.

Stationary External Electric Field-Mimicking the Solvent Effect on the Ground-State Tautomerism and Excited-State Proton Transfer in 8-(Benzo[d]thiazol-2-yl)quinolin-7-ol

The effect of the external electric field on the ground-state tautomerism in 8-(benzo[d]thiazol-2-yl)quinolin-7-ol has been studied by using density functional theory. The compound exists as an enol tautomer (off state) and under the influence of the external electric field a long-range intramolecular proton transfer can occur, placing the tautomeric proton at the quinolyl nitrogen atom (on state). This is a result of the much higher dipole moment of the end keto tautomer and indicates that the external electric field can be used to mimic the implicit solvent effect in tautomeric systems. In the excited state, the further stabilization of the most polar on state leads to a situation when the excited-state intramolecular proton transfer becomes impossible, limiting the intramolecular rotation to the conical intersection region.

Regulating and controlling the stepwise ESDPT channel of BP(OH)2DCEt2 using the strategy of solvent polarity and external electric field

Excited state double proton transfer (ESDPT) has attracted great scientific interest because of its excellent luminescent properties. However, the complex process of ESDPT has plagued theoretical and experimental scientists for a long time and has become a hot issue. In this work, the ESDPT process of 2,2'-bipyridine-3,3'-diol-5,5'-dicarboxylic acid ethyl ester (BP(OH)2DCEt2) is systematically studied and the regulation of the ESDPT process is further realized. The potential energy curves indicate that BP(OH)2DCEt2 shows the characteristics of stepwise ESDPT in different polar solvents. The increase in solvent polarity will be beneficial to the stepwise ESDPT reaction. Regrettably, it is not possible to distinguish the specific stepwise transfer path of the BP(OH)2DCEt2 molecule due to the symmetry of the potential energy surface along the diagonal. On this basis, we proposed a method to control and regulate the stepwise ESDPT path using an external electric field. The results show that the increase of external electric field intensity is favorable to stepwise ESDPT. It is interesting to note that applying an external electric field in a specific direction will effectively distinguish stepwise ESDPT reaction paths. Therefore, this work not only helps to understand the mechanism of ESDPT, but also contributes to regulation and design of new luminescent materials with excellent luminescent properties.

OEEF-Driven Intramolecular Self-Redox of Superalkali Rb3BeB6Be'Rb'3: A High-Performance Candidate for NLO Molecular Switch

To provide a novel intramolecular self-redox switch, a boron-based sandwich-like complex Rb3BeB6Be'Rb'3 is achieved by using theoretical computations. An applicable oriented external electric field (OEEF) can result in the occurrence of intramolecular self-redox (IMSR) with a long-range electron transfer from tetrahedral Be'Rb'3 to Rb3Be and subsequently [Rb3Be]3+[B6]6-[Be'Rb'3]3+ (D3d) changes to [Rb3Be]2+[B6]6-[Be'Rb'3]4+ (C3v), accompanying high-performance NLO switchable effect for both static and dynamic first hyperpolarizability (β0). [Rb3Be]3+[B6]6-[Be'Rb'3]3+ (off-form) owns zero of dipole moment (μ0) and β0, while [Rb3Be]2+[B6]6-[Be'Rb'3]4+ (on-form) exhibits a μ0 of 3.36 D and a β0e of 2.18 × 105 au. The different dynamic first hyperpolarizabilities between [Rb3Be]3+[B6]6-[Be'Rb'3]3+ and [Rb3Be]2+[B6]6-[Be'Rb'3]4+ are also significant. This indicates that Rb3BeB6Be'Rb'3 is a potential candidate for an IMSR NLO switch.

External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C+:C Base Pair

In this work, we computationally designed a set of nitroxide diradical base pairs (rC⁺:rC) to propose promising magnetic building blocks for spintronic or magnetic molecular materials. C⁺:C12 is found to possess a considerably large antiferromagnetic-like (AFM-like) spin-coupling magnitude (J = -3286.681 cm^-1) and sensitive magnetic responses to the external electric field. Especially, the presence of the Y direction field that is oriented perpendicular to intermolecular hydrogen bonds has the greatest influence on the magnetic exchange interaction (J being from -2549.578 to -4231.286 cm^-1, ΔJ_Y = 1681.708 cm^-1), which could be understood by two simultaneously occurring effects. On the one hand, the external electric field in the -Y direction can regulate the charge polarization of negative and positive electrostatic potentials on C12 moiety and further facilitate the spin transport property. On the other hand, with increasing electric field strength on the -Y axis, the spin density on diradical sources diminishes and that on the coupler increases, which can lead to a homogenous spin-density distribution. The achieved understanding provides a new strategy for designing self-assembly magnetic nanomaterials or nanodevices and enhancing the AFM coupling through the assistance of external electric field.

How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer's and Other Senile Plaques?

Alzheimer's disease is one of the most common neurodegenerative conditions, which are ascribed to extracellular accumulation of β-amyloid peptides into plaques. This phenomenon seems to typify other related neurodegenerative diseases. The present study uses classical molecular-dynamics simulations to decipher the aggregation-disintegration behavior of β-amyloid peptide plaques in the presence of static and oscillating oriented external electric fields (OEEFs). A long-term disintegration of such plaques is highly desirable since this may improve the prospects of therapeutic treatments of Alzheimer's disease and of other neurodegenerative diseases typified by senile plaques. Our study illustrates the spontaneous aggregation of the β-amyloid, its prevention and breakdown when OEEF is applied, and the fate of the broken aggregate when the OEEF is removed. Notably, we demonstrate that the usage of an oscillating OEEF on β-amyloid aggregates appears to lead to an irreversible disintegration. Insight is provided into the root causes of the various modes of aggregation, as well as into the different fates of OEEF-induced disintegration in oscillating vs static fields. Finally, our simulation results are compared to the well-established TTFields and the Deep Brain Stimulation (DBS) therapies, which are currently used options for treatments of Alzheimer's disease and other related neurodegenerative diseases.

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.

A catastrophe theory-based model for optimal control of chemical reactions by means of oriented electric fields

The effect of oriented external electric fields (OEEF) on chemical reactivity has been studied theoretically and computationally in the last decades. A central goal in this research area is to predict the orientation and the smallest amplitude electric field that renders a barrierless chemical process with the smallest possible strength. Recently, a model to find the optimal electric field has been proposed and described (Bofill JM et al., J. Chem. Theory Comput. 18:935, 2022). We here proof that this model is based on catastrophe and optimum control theories. Based on both theories a technical treatment of the model is given and applied to a two-dimensional generic example that provides insight into its nature and capability. Finally, the model is applied to determine the optimal OEEF for the trans-to-cis isomerization of a [3]cumulene derivative.

Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity

The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol⁻¹) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns⁻¹, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors.

Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.

Influence of an Oriented External Electric Field on the Mechanism of Double Proton Transfer between Pyrazole and Guanidine: from an Asynchronous Plateau Transition State to a Synchronous or Stepwise Mechanism

The double proton transfer (DPT) reaction between pyrazole and guanidine, a concerted reaction but strongly asynchronous and presenting a "plateau transition region", has been theoretically reinvestigated in the presence of an external uniform electric field. First, we computed the reaction path by DFT and proposed a very detailed description of the constitutive electronic events, based on the ELF topology and the bond evolution theory. Then, we studied the effect of an oriented external electric field (OEEF) on the reaction mechanism, for an OEEF oriented along the proton transfer axis. We observe that in one direction, the DPT reaction can be transformed into a stepwise reaction, going through a stabilized single proton transferred intermediate. Contrarily, the two proton transfers occur simultaneously when the electric field is applied in the opposite direction. In the latter case, the order in which the two protons are transferred in the same elementary step can even be reversed if the OEEF is intense enough. Finally, it has been shown that the evolution of the double proton transfer reaction in the presence of an electric field could be quantitatively anticipated by analyzing the ELF value at the bifurcation point between V(A, H) proton donor and V(B) proton acceptor of the double hydrogen bonded complex in the entrance channel.

Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1-H at a Watson-Crick edge and non-statistical dissociation

It has been shown previously in protonated, deprotonated and ionized guanine-cytosine base pairs that intra-base pair proton transfer from the N1-H at the Watson-Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure-kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), i.e., [9MG·9MG]˙⁺, [9MOG·9MG]˙⁺ and [9MOG·9MOG]˙⁺. Experimentally, collision-induced dissociation tandem mass spectrometry coupled with an electrospray ionization (ESI) source was used for the formation of base-pair radical cations, followed by detection of dissociation product ions and cross sections in the collisions with Xe gas under single ion-molecule collision conditions and as a function of the center-of-mass collision energy. Computationally, density functional theory and coupled cluster theory were used to calculate and identify probable base-pair structures and intra-base pair proton transfer and hydrogen transfer reactions, followed by kinetics modeling to explore the properties of dissociation transition states and kinetic factors. The significance of this work is twofold: it provides insight into base-pair opening kinetics in three biologically-important, non-canonical systems upon oxidative and ionization damage; and it links non-statistical dissociation to intra-base pair proton-transfer originating from the N1-H at the Watson-Crick edge of 8-oxoguanine, enhancing understanding towards the base-pair fragmentation assisted by proton transfer.

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.

Mechanistic Insights into Visible-Light-Driven Dearomative Fluoroalkylation Mediated by an Electron Donor-Acceptor Complex

Electron donor-acceptor (EDA) complex photochemistry has become a burgeoning topic in the synthetic radical chemistry mediated by visible light; however, the theoretical insights into the reaction mechanisms are limited. Herein, accurate electronic structure calculations at the CASPT2//CASSCF/PCM level of theory were performed to investigate the paradigm example of EDA complex-enabled photoreaction for visible-light-driven dearomative perfluoroalkylation of β-naphthol. The excitation energy levels of the EDA complex are controlled by noncovalent interactions because the photoinduced intermolecular charge is enhanced when the noncovalent interaction becomes weaker, leading to the broad spectra ranging from UVA (<380 nm) to visible light (>500 nm). The competitiveness of the radical-radical coupling over the radical chain pathway is also regulated due to the tunable radical concentrations varying the excitation wavelength.

Double Proton Transfer during a Novel Tertiary α-Ketol Rearrangement in Ketol-Acid Reductoisomerase: A Water-Mediated, Metal-Catalyzed, Base-Induced Mechanism

(KARI) catalyzes the conversion of (S)-2-acetolactate or (S)-2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate, the second step in the biosynthesis of branched chain amino acids (BCAAs). Because the BCAA biosynthetic pathway is present in bacteria, plants, and fungi, but absent in animals, it is an excellent target for the development of new-generation antibiotics and herbicides. Nevertheless, the mechanism of the KARI-catalyzed reaction has not yet been fully solved. In this study, we used iterative molecular dynamics (MD) flexible fitting-Rosetta techniques to optimize the three-dimensional solution structure of archaea KARI from Sulfolobus solfataricus (Sso-KARI) determined from cryo-electron microscopy. On the basis of the structure of the Sso-KARI/2Mg²⁺/NADH/(S)-2-acetolactate complex, we deciphered the catalytic mechanism of the KARI-mediated reaction through hybrid quantum mechanics/molecular mechanics MD simulations in conjunction with umbrella sampling. With an activation energy of only 6.06 kcal/mol, a water-mediated, metal-catalyzed, base-induced (WMMCBI) mechanism was preferred for deprotonation of the tertiary OH group of (S)-2-acetolactate in Sso-KARI. The WMMCBI mechanism for double proton transfer occurred within a proton wire route with two steps involving the formation of hydroxide: (i) Glu233 served as a general base to deprotonate the Mg²⁺-bound water, forming a hydroxide-coordinated Mg²⁺ ion; (ii) this hydroxide ion acted as a strong base that rapidly deprotonated the ternary OH group of the substrate. In contrast, the direct deprotonation of the substrate by Glu233 was kinetically unfavorable. This mechanism suggests a novel approach for designing catalysts for deprotonation and provides clues for the development of new-generation antibiotics and herbicides.

Kinetic Study of Transition Mutations from G-C to A-T Base Pairs in Watson-Crick DNA Base Pairs: Double Proton Transfers

According to the Löwdin model [ Rev. Mod. Phys. 1963, 35, 724-732], the Watson-Crick guanine-cytosine (G-C) base pair is tautomerized (G*-C*) with a small probability and then replication of G*-C* produces G*-thymine (T) and adenine (A)-C* base pairs. On the basis of this model and our previous work [ J. Phys. Chem. B 2020, 124, 1715-1722], we first calculated the intrinsic reaction coordinates from G*-T to G-T* using density functional theory and evaluated the probability of G*-T tautomerization to G-T* by double proton transfer (DPT) on the basis of the transition state theory. Similarly, we calculated the probability of A-C* tautomerization to A*-C by DPT. Then, according to these probabilities, we calculated the probability of transition mutations from G-C to A-T after 2 replications. The calculated probability was 1.31 × 10^-8, a value consistent with the mutation rate previously reported by Drake et al. [ Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 7160-7164]. Our results suggest that DPT is one cause of the G-C → A-T transition. To investigate differences in the optical properties between G*-T and G-T* and between A-C* and A*-C, we also evaluated the infrared absorption spectra and Raman intensities for these base pairs.

Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine-1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework

We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine-1-methylcytosine base pair (HG-[9MG·1MC + H]+), which aims to address the mystery of the literature reported "anomaly" in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H]+ (reported recently by Sun et al.; Phys. Chem. Chem. Phys., 2020, 22, 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice-Ramsperger-Kassel-Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H]+ over [9MG + H]+ in the fragment ions of HG-[9MG·1MC + H]+. The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointed the origin of the statistical kinetics of HG-[9MG·1MC + H]+vs. the non-statistical behavior of WC-[9MG·1MC + H]+ in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3' of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e., HG-[9MG·1MC + H]+·H2O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H]+, secondary methanol elimination was observed via the SN2 reaction of water with nucleobase methyl groups.

The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair

The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.

Switching from an electride-like molecule to the molecular electride K-F6C6H6 driven by an oriented external electric field

The exploration of innovative molecular switches has resulted in large developments in the field of molecular electronics. Focusing on a single molecular switch with different forms exhibiting different electride features, potassium-atom-doped all-cis 1,2,3,4,5,6-hexafluorocyclohexane K-F6C6H6 was studied theoretically. It was found that an oriented external electric field can drive excess electron transfer from the region outside of the K atom to that outside of F6C6H6. Subsequently, the electride-like molecule K-F6C6H6 (1) switches into the molecular electride K-F6C6H6e- (3) through another electride-like molecule K-F6C6H6 (2). The static first hyperpolarizabilities (β0) are increased over 12- and 5-fold when moving from 1 to 2 and 3, respectively. The rise of each β0 value constitutes an order of magnitude improvement. Between them, the different β0 values suggest that K-F6C6H6 is a good candidate for use as a multiple-response nonlinear optics switch. The order of the β0 values of 1-4 for M-F6C6H6 (M = Li and Na) coincide with that of K-F6C6H6, also exhibiting a switch effect.

Switch chemistry at cryogenic conditions: quantum tunnelling under electric fields

While the influence of intramolecular electric fields is a known feature in enzymes, the use of oriented external electric fields (EEF) to enhance or inhibit molecular reactivity is a promising topic still in its infancy. Herein we will explore computationally the effects that EEF can provoke in simple molecules close to the absolute zero, where quantum tunnelling (QT) is the sole mechanistic option. We studied three exemplary systems, each one with different reactivity features and known QT kinetics: π bond-shifting in pentalene, Cope rearrangement in semibullvalene, and cycloreversion of diazabicyclohexadiene. The kinetics of these cases depend both on the field strength and its direction, usually giving subtle but remarkable changes. However, for the cycloreversion, which suffers large changes on the dipole through the reaction, we also observed striking results. Between the effects caused by the EEF on the QT we observed an inversion of the Arrhenius equation, deactivation of the molecular fluxionality, and stabilization or instantaneous decomposition of the system. All these effects may well be achieved, literally, at the flick of a switch.

External Electric Fields Interrupt the Concerted Cope Rearrangement of Semibullvalene

The topic of this paper is whether the mechanism of the degenerate Cope rearrangement of semibullvalene can be affected by the presence of electrostatic fields. Herein, we report that the shape of the energy surface, as demonstrated by an "interrupted" (stepwise) mechanism, is altered in the presence of a copper cation, Cu⁺. Natural bond-orbital and block-localized wave-function energy decomposition analyses suggest that orbital and electrostatic interactions play a major role in altering the shape of the energy surface. Applying additional external electric fields (EEFs) induces a significant change to the energy surface with Cu⁺ present but negligible effects in the absence of Cu⁺. These findings are consistent with recent studies that demonstrate that EEFs more readily stabilize/destabilize systems with larger, more polarizable, dipole moments.

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.

Electric field induced intra-molecular self-redox: superalkali Li3N3Mg as a candidate for NLO molecular switches

A novel intra-molecular self-redox switch, Li₃N₃Mg, is constructed theoretically. Our investigation showed that a suitably oriented external electric field (OEEF) can drive a long-range excess electron transfer from Mg atoms to Li₃ rings. And subsequently, an interesting intra-molecular self-redox from Li₃²⁺N₃^3-Mg⁺ to Li₃⁺N₃^3-Mg²⁺ accompanying the large different electronic static first hyperpolarizability (β) is exhibited. The increase of the β value constitutes an order of magnitude improvement from Li₃²⁺N₃^3-Mg⁺ (34 986 a.u.) to Li₃⁺N₃^3-Mg²⁺ (101 225 a.u.), which indicates that Li₃N₃Mg is a good candidate for a self-redox NLO molecular switch.

Density functional theory studies on cytosine analogues for inducing double-proton transfer with guanine

To induce double-proton transfer (DPT) with guanine in a biological environment, 12 cytosine analogues (Ca) were formed by atomic substitution. The DPT reactions in the Watson-Crick cytosine-guanine model complex (Ca₀G) and 12 modified cytosine-guanine complexes (Ca_1-12G) were investigated using density functional theory methods at the M06-2X/def2svp level. The intramolecular proton transfers within the analogues are not facile due to high energy barriers. The hydrogen bond lengths of the Ca_1-12G complexes are shorter than those in the Ca₀G complex, which are conducive to DPT reactions. The DPT energy barriers of Ca_1-12G complexes are also lower than that of the Ca₀G complex, in particular, the barriers in the Ca₇G and Ca₁₁G complexes were reduced to -1.33 and -2.02 kcal/mol, respectively, indicating they are significantly more prone to DPT reactions. The DPT equilibrium constants of Ca_1-12G complexes range from 1.60 × 10⁰ to 1.28 × 10⁷, among which the equilibrium constants of Ca₇G and Ca₁₁G are over 1.0 × 10⁵, so their DPT reactions may be adequate. The results demonstrate that those cytosine analogues, especially Ca₇ and Ca₁₁, are capable of inducing DPT with guanine, and then the guanine tautomer will form mismatches with thymine during DNA replication, which may provide new strategies for gene therapy.

Manipulation of Diatomic Molecules with Oriented External Electric Fields: Linear Correlations in Atomic Properties Lead to Nonlinear Molecular Responses

Oriented external electric fields (OEEFs) have been shown to have great potential in being able to provide unprecedented control of chemical reactions, catalysis, and selectivity with applications ranging from H₂ storage to molecular machines. We report a theoretical study of the atomic origins of molecular changes because of OEEFs since understanding the characteristics of OEEF-induced couplings between atomic and molecular properties is an important step toward comprehensive understanding of the effects of strong external fields on the molecular structure, stability, and reactivity. We focus on the atomic and molecular (bond) properties of a set of homo- (H₂, N₂, O₂, F₂, and Cl₂) and heterodiatomic (HF, HCl, CO, and NO) molecules under intense external electric fields in the context of quantum theory of atoms in molecules (QTAIM). It is shown that the atomic properties (atomic charges, energies, and localization indices) correlate linearly with the field strengths, but molecular properties (bond length, electron density at the bond critical point, and electron delocalization index) exhibit nonlinear responses to the imposed fields. In particular, the changes in the electron density distribution alter the shapes and locations of the zero-flux surfaces, atomic volumes, atomic electron population, and localization/delocalization indices. The topography and topology of the molecular electrostatic potential undergo dramatic changes. External fields also perturb the covalent-polar-ionic characteristic of the studied chemical bonds, hallmarking the impact of electric fields on the stability and reactivity of chemical compounds. The findings are well-rationalized within the framework of the QTAIM and form a coherent conceptual understanding of these effects in prototypical diatomic molecules.

Tipping the balance: theoretical interrogation of divergent extended heterolytic fragmentations

Herein we interrogate a type of heterolytic fragmentation reaction called a 'divergent fragmentation' using density functional theory (DFT), natural bond orbital (NBO) analysis, ab initio molecular dynamics (AIMD), and external electric field (EEF) calculations. We demonstrate that substituents, electrostatic environment and non-statistical dynamic effects all influence product selectivity in reactions that involve divergent fragmentation pathways. Direct dynamics simulations reveal an unexpected post-transition state bifurcation (PTSB), and EEF calculations suggest that some transition states for divergent pathways can, in principle, be selectively stabilized if an electric field of the correct magnitude is oriented appropriately.

Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues

Non-statistical dissociation of a protonated guanine–cytosine Watson–Crick base pair.

Fullerene-Based Switching Molecular Diodes Controlled by Oriented External Electric Fields

Employing multiscale in silico modeling, we propose switching molecular diodes on the basis of endohedral fullerenes (fullerene switching diode, FSD), encapsulated with polar molecules of general type MX (M: metal, X: nonmetal) to be used for data storage and processing. Here, we demonstrate for MX@C₇₀ systems that the relative orientation of enclosed MX with respect to a set of electrodes connected to the system can be controlled by application of oriented external electric field(s). We suggest systems with two- and four-terminal electrodes, in which the source and drain electrodes help the current to pass through the device and help the switching between the conductive states of FSD via applied voltage. The gate electrodes then assist the switching by effectively lowering the energy barrier between local minima via stabilizing the transition state of switching process if the applied voltage between the source and drain is insufficient to switch the MX inside the fullerene. Using nonequilibrium Green's function combined with density functional theory (DFT-NEGF) computations, we further show that conductivity of the studied MX@C₇₀ systems depends on the relative orientation of MX inside the cage with respect to the electrodes. Therefore, the orientation of the MX inside C₇₀ can be both enforced ("written") and retrieved ("read") by applied voltage. The studied systems thus behave like voltage-sensitive switching molecular diodes, which is reminiscent of a molecular memristor.