Electronic Structure and Hole Transfer of All B-DNA Dimers and Homopolymers, via the Fishbone-Wire Model

We employ the Tight Binding Fishbone-Wire Model to study the electronic structure and coherent transfer of a hole (the absence of an electron created by oxidation) in all possible ideal B-DNA dimers as well as in homopolymers (one base pair repeated along the whole sequence with purine on purine). The sites considered are the base pairs and the deoxyriboses, with no backbone disorder. For the time-independent problem, we calculate the eigenspectra and the density of states. For the time-dependent problem after oxidation (i.e., the creation of a hole either at a base pair or at a deoxyribose), we calculate the mean-over-time probabilities to find the hole at each site and establish the frequency content of coherent carrier transfer by computing the Weighted Mean Frequency at each site and the Total Weighted Mean Frequency of a dimer or polymer. We also evaluate the main oscillation frequencies of the dipole moment along the macromolecule axis and the relevant amplitudes. Finally, we focus on the mean transfer rates from an initial site to all others. We study the dependence of these quantities on the number of monomers that are used to construct the polymer. Since the value of the interaction integral between base pairs and deoxyriboses is not well-established, we treat it as a variable and examine its influence on the calculated quantities.

Charge transport properties of ideal and natural DNA segments, as mutation detectors

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)_n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.

Cyclo[18]carbon including zero-point motion: ground state, first singlet and triplet excitations, and hole transfer

Recent synthesis of cyclo[18]carbon has spurred increasing interest in carbon rings. We focus on a comparative inspection of ground and excited states, as well as of hole transfer properties of cumulenic and polyynic cyclo[18]carbon via Density Functional Theory (DFT), time-dependent DFT (TD-DFT) and real-time time-dependent DFT (RT-TDDFT). Zero-point vibrations are also accounted for, using a Monte Carlo sampling technique and a less exact, yet mode-resolved, quadratic approximation. The inclusion of zero-point vibrations leads to a red-shift on the HOMO-LUMO gap and the first singlet and triplet excitation energies of both conformations, correcting the values of the 'static' configurations by 9% to 24%. Next, we oxidize the molecule, creating a hole at one carbon atom. Hole transfer along polyynic cyclo[18]carbon is decreased in magnitude compared to its cumulenic counterpart and lacks the symmetric features the latter displays. Contributions by each mode to energy changes and hole transfer between diametrically opposed atoms vary, with specific bond-stretching modes being dominant.

Treatment with a fixed dose combination for cardiovascular disease-more than a health benefit?

Background

Despite the proven benefits of cardiovascular disease medication, adherence to treatment remains poor. Fixed-dose combinations (FDC) have been proposed as a measure to enhance adherence.

Objective

To assess compliance to treatment with an FDC, consisting of acetylsalicylic acid, atorvastatin and ramipril, and to gauge its impact on cardiovascular risk factors.

Methods

This was a prospective, multicenter, observational, phase 4 study conducted for 6 months in Greece. 1444 participants (67% males, mean age 63.7 years old) that were prescribed the FDC for primary or secondary prevention were included in the analysis. Descriptive statistical analysis was performed to analyze clinical, sociodemographic and safety parameters.

Results

Approximately equal number of participants was recruited in the primary and secondary prevention group. The majority of patients were overweight and hypertensive. Dosing compliance was 88.6% at 3 months and 86.8% at 6 months. Adherence to treatment was 99.1% at 3 months and 97.6% at 6 months. Statistically significant changes at 6 months compared to baseline were documented in systolic/diastolic blood pressure of 15.7/7.5 mmHg and LDL-c of 32.6 mg/dl, in both CVD and non-CVD participants and in total population as well. The total 10-year risk for CV events was reduced by 34.1% at 6 months. Only 1.2% of the participants reported an adverse event and 0.8% an adverse event reaction.

Conclusions

Among patients with or without CVD, the use of acetylsalicylic acid, atorvastatin and ramipril FDC resulted in good medication adherence at 6 months and statistically significant improvements in blood pressure, total cholesterol and LDL levels.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Galenica SA

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

Hole Transfer in Open Carbynes

We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) "ground state energy" of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results.

Publisher's Note: Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model [Phys. Rev. E 94, 062403 (2016)]

This corrects the article DOI: 10.1103/PhysRevE.94.062403.

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer

We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of N monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the highest occupied molecular orbital (HOMO) eigenspectrum and the lowest unoccupied molecular orbital (LUMO) eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate k. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare k ( N ) of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport

We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A), on the same strand, i.e., our prototype binary alphabet is {G,A}. Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization, and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients, and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.

Electronic structure and charge transport properties of atomic carbon wires

Atomic carbon wires represent the ultimate one-atom-thick one-dimensional structure.

Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers

We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency [Formula: see text]-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model

We employ two tight-binding (TB) approaches to systematically study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of N monomers (base pairs): (I) at the base-pair level, using the onsite energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the onsite energies of the bases and the hopping integrals between neighboring bases, i.e., an extended ladder model since we also include diagonal hoppings. We solve a system of M (matrix dimension) coupled equations [(I) M=N, (II) M=2N] for the time-independent problem, and a system of M coupled first order differential equations for the time-dependent problem. We perform a comparative study of stationary and time-dependent aspects of the two TB variants, using realistic sets of parameters. The studied properties include HOMO and LUMO eigenspectra, occupation probabilities, density of states and HOMO-LUMO gaps as well as mean over time probabilities to find the carrier at each site [(I) base pair or (II) base], Fourier spectra, which reflect the frequency content of charge transfer, and pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.

Publisher's Note: Unbiased charge oscillations in B-DNA: Monomer polymers and dimer polymers [Phys. Rev. E 92, 032725 (2015)]

This corrects the article DOI: 10.1103/PhysRevE.92.032725.

Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers

We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair B-DNA segment. We study highest occupied molecular orbital and lowest unoccupied molecular orbital eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power-law fits k(N) are computed; generally power-law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N) becomes steeper and show the range covered by β and η. Finally, for both the time-independent and the time-dependent problems, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.