Equilibrium Charge Distribution in a Finite Chain with a Trapping Site

The paper considers the problem of the distribution of a quantum particle in a classical one-dimensional lattice with a potential well. The cases of a rigid chain, a Holstein polaron model, and a polaron in a chain with temperature are investigated by direct modeling at fixed parameters. As is known, in the one-dimensional case, a particle is captured by an arbitrarily shallow potential well with an increase of the box size. In the case of a finite chain and finite temperatures, we have quite the opposite result, when a particle, being captured in a well in a short chain, turns into delocalized state with an increase in the chain length. These results may be helpful for further understanding of charge transfer in DNA, where oxoguanine can be considered as a potential well in the case of hole transfer when for excess electron transfer it is thymine dimer.

Stacking Effects on Charge Transfer Dynamics in Fluctuating DNA

Base-stacked structure is an important feature of DNA molecules. But dynamics study on the influences of the stacking effects on charge transfer in DNA is yet rare.In this article, a general rule about the relationship of onsite energies of same bases in a stack is derived by H ̈uckel theory. It is found that the base in the middle position of the stack has lower onsite energy than the bases at the terminals due to squeezing effect, which is different from previous studied neighboring base effect. The former is along-range effect while the latter acts in a short range. Semiempirical MNDO calculations on (A:T) n (n=1∼10) systems verfied the H ̈uckel analysis. From this perspective,the so-called incoherent hopping mechanism is actually somewhat coherent due to the squeezing effect. To understand these stacking effects on charge transfer in DNA,a cross-scale method which combines classical MD simulations, quantum mechanism calculations, Marcus electron transfer theory and kinetic Monte Carlo simulations is developed and applied on hole dynamics in (A:T) n (G:C) (n=1∼10) systems. Although no superexchange mechanism is explicitly involved in the studied systems, a crossover from strong to weak distance-dependency of hole arrival rates, which is an experimentally observed property of hole dynamics in DNA and is thought an evidence of the conversion from superexchange to hopping mechanism, also appears. We attribute it to the stacking effects. Such a result provides a new idea on explaining the crossover of different distance-dependencies of charge transfer rates in DNA. In addition, the squeezing effect may be a new driving force for long-range charge transfer. At the same time, some technical methods developed in the dynamics, e.g. calculations of onsite energies and electronic couplings in a stack, and simulated hole dynamics, etc.,can be generalized to other complex molecular systems with charge transfer behaviors.<br><br>

Stacking Effects on Charge Transfer Dynamics in Fluctuating DNA

Base-stacked structure is an important feature of DNA molecules. But dynamics study on the influences of the stacking effects on charge transfer in DNA is yet rare.In this article, a general rule about the relationship of onsite energies of same bases in a stack is derived by H ̈uckel theory. It is found that the base in the middle position of the stack has lower onsite energy than the bases at the terminals due to squeezing effect, which is different from previous studied neighboring base effect. The former is along-range effect while the latter acts in a short range. Semiempirical MNDO calculations on (A:T) n (n=1∼10) systems verfied the H ̈uckel analysis. From this perspective,the so-called incoherent hopping mechanism is actually somewhat coherent due to the squeezing effect. To understand these stacking effects on charge transfer in DNA,a cross-scale method which combines classical MD simulations, quantum mechanism calculations, Marcus electron transfer theory and kinetic Monte Carlo simulations is developed and applied on hole dynamics in (A:T) n (G:C) (n=1∼10) systems. Although no superexchange mechanism is explicitly involved in the studied systems, a crossover from strong to weak distance-dependency of hole arrival rates, which is an experimentally observed property of hole dynamics in DNA and is thought an evidence of the conversion from superexchange to hopping mechanism, also appears. We attribute it to the stacking effects. Such a result provides a new idea on explaining the crossover of different distance-dependencies of charge transfer rates in DNA. In addition, the squeezing effect may be a new driving force for long-range charge transfer. At the same time, some technical methods developed in the dynamics, e.g. calculations of onsite energies and electronic couplings in a stack, and simulated hole dynamics, etc.,can be generalized to other complex molecular systems with charge transfer behaviors.<br><br>

The Watson-Crick rare tautomer hypothesis of mutations and reality

Background: In their Nature's seminal work (Nature. 1953;171:737), J.D. Watson and F.H.C. Crick noted that the structure of DNA admits a so-called tautomeric model of spontaneous point mutations. This work reported at the conference "Nanobiophysics-2019" (Kiev) as a plenary report, is actually an attempt to answer the following questions: (i) "Yes, the tautomerism of the bases is a very attractive model, but how important is it in mutagenesis?" by Morgan (Morgan AR. Trends Biochem. Sci. 1993;18:160–163); (ii) What reality does the rare tautomeric mutation model describe? The structure [А×Т]WC was selected in the work. Developing the previously proposed mutation model×of the Watson-Crick pair [А×Т]WC due to the shift of the bases in the pair relative to each other and the interconnection hydrogen bonds (Kryachko ES, Sabin JR. Int. J. Quantum Chem. 2003;91:695–710), it is shown that some resultant structures possess the electron affinity that is 1.7 times higher compared to the canonical pair, which is definitely of interest in the view of the numerous phenomena associated with a charge transfer in and attachment of an electron to DNA. Objectives: Answer the questions raised in the Background, and show the realism of the tautomeric [А×Т]WC-mutation model modified in the present work on the example of the Watson-Crick pair [А×Т]WC that is dubbed as a pair-tautomerism model. Materials and Methods: The key method is a computer simulation based on the density functional method. All calculations performed in the present work use the package of programs GAUSSIAN with the density functional method invoking the Becke-Lee-Yang-Parr density functional, B3LYP. Results: The paper shows the existence and stability of paired tautomeric mutations in a pair of adenine-thymine and investigates to what wobble pairs it can lead. It is also shown that, due to the specific structure of the paired tautomeric mutation of the adenine-thymine pair, the mutation possesses a larger electronic affinity in comparison with the pair that it generates, and thus can be observed in reality and through it one can explain a number of phenomena of charge transfer in DNA, which, again, emphasizes its reality. Conclusions: On the one hand, a generalization of the Watson-Crick tautomeric hypothesis, proposed in this work, specifically for the adenine-thymine pair, the name of the paired tautomeric mutation. This mutation refers to dipole-binding-electron systems, which implies their high adiabatic electron affinity. The latter, on the other hand, emphasizes the realism of the proposed mutational model and its possible application to the explanation of the phenomena of charge transfer in DNA and the processes of attachment electron to DNA.

Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

Charge diffusion in homogeneous molecular chains based on the analysis of generalized frequency spectra in the framework of the Holstein model

We analyzed numerically computed velocity autocorrelation functions and generalized frequency spectra of charge distribution in homogeneous DNA sequences at finite temperature. The autocorrelation function and generalized frequency spectrum (frequency-dependent diffusion coefficient) are phenomenologically introduced based on the functional of mean-square displacement of the charge in DNA. The charge transfer in DNA was modeled in the framework of the semi-classical Holstein model. In this model, DNA is represented by a chain of oscillators placed into thermostat at a given temperature that is provided by the additional Langevin term. Correspondence to the real DNA is provided by choice of the force parameters, which are calculated with quantum-chemical methods. We computed the diffusion coefficient for all homogenous DNA chains with respect to the temperature and found a special scaling of independent variables that the temperature dependence of the diffusion coefficient for different homogenous DNA is almost similar. Our calculations suggest that for all the sequences, only one parameter of the system is mainly responsible for the charge kinetics. The character of individual motions contributing to the charge mobility and temperature-dependent regimes of charge distribution is determined.

Numerical Simulation of Small Radius Polaron in a Chain with Random Perturbations

We consider the dynamics of polaron in a chain using computational experiment. The temperature, which is simulated by random Langevin-type perturbations, and influence of external electric field are taking into account. In a sufficiently long unperturbed chain, the displacement of the center of mass of the polaron and its velocity does not depend on its length. In the semiclassical Holstein model, which is applied for simulations of charge transfer in DNA, the region of polaron existence in the thermodynamic equilibrium state depends not only on temperature, but also on the chain length. Therefore, when modeling dynamics from polaron initial data, the time dependences of the average displacement of the charge mass center at the same temperature are different for chains of different lengths. According to the results of computational experiment, for polaron of large radius the time dependence of the “average polaron displacement”, which takes into account only the polaron peak and its position, for chains of different lengths behaves almost equally at time intervals until the polaron will destroyed. The same slope of the polaron displacement allows us to estimate the average polaron velocity. The results of calculations demonstrate that in Holstein model at zero temperature, the mobility value of the large radius polaron is small but non-zero.