Static and dynamic aspects of DNA charge transfer: a theoretical perspective

Protonation and orientation: a computational approach to cocaine diffusion through a model membrane

We study the diffusion of cocaine through a DMPC lipid bilayer as an example of a protonable, amphiphilic molecule passing a biological membrane. Using classical molecular dynamics simulations, the free...

Monte Carlo simulation and thermodynamic integration applied to protein charge transfer

We introduce a combination of Monte Carlo simulation and thermodynamic integration methods to address a model problem in free energy computations, electron transfer in proteins. The feasibility of this approach is tested using the ferredoxin protein from Clostridium acidurici. The results are compared to numerical solutions of the Poisson-Boltzmann equation and data from recent molecular dynamics simulations on charge transfer in a protein complex, the NrfHA nitrite reductase of Desulfovibrio vulgaris. Despite the conceptual and computational simplicity of the Monte Carlo approach, the data agree well with those obtained by other methods. A link to experiments is established via the cytochrome subunit of the bacterial photosynthetic reaction center of Rhodopseudomonas viridis.

The quality of health services provided to remote dwelling aboriginal infants in the top end of northern Australia following health system changes: a qualitative analysis

Background

In Australia the health outcomes of remote dwelling Aboriginal infants are comparable to infants in developing countries. This research investigates service quality, from the clinicians’ perspective and as observed and recorded by the researcher, in two large Aboriginal communities in the Top End of northern Australia following health system changes.

Methods

Data were collected from semi-structured interviews with 25 clinicians providing or managing child health services in the two study sites. Thirty hours of participant observation was undertaken in the ‘baby-rooms’ at the two remote health centres between June and December 2012. The interview and observational data, as well as field notes were integrated and analysed thematically to explore clinicians’ perspectives of service delivery to infants in the remote health centres.

Results

A range of factors affecting the quality of care, mostly identified before health system changes were instigated, persisted. These factors included ineffective service delivery, inadequate staffing and culturally unsafe practices. The six themes identified in the data: ‘very adhoc’, ‘swallowed by acute’, ‘going under’, ‘a flux’, ‘a huge barrier’ and ‘them and us’ illustrate how these factors continue, and when combined portray a ‘very chaotic system’.

Conclusion

Service providers perceived service provision and quality to be inadequate, despite health system changes. Further work is urgently needed to improve the quality, cultural responsiveness and effectiveness of services to this population.

Electronic supplementary material

The online version of this article (doi:10.1186/s12887-017-0849-1) contains supplementary material, which is available to authorized users.

Organic semiconductors: impact of disorder at different timescales

The charge transport in organic materials, from molecular crystals to polymers, is determined by their degree of disorder. The dynamic disorder in ideal molecular crystals at room temperature and the static disorder in disordered polymers are just two limiting cases of the timescale of the fluctuations in the electronic Hamiltonian caused by nuclear motions. In fact, a very large number of important materials (e.g. liquid crystalline semiconductors) are actually in an intermediate regime where the disorder is neither purely static nor purely dynamic. This Minireview discusses the recent contribution of computational chemistry (molecular dynamics and quantum chemistry) to the characterization of these transport regimes and outlines the theoretical methods that can be used to relate the system characteristics to the measurable mobility.

A Direct Simulation of Adiabatic Charge Transfer Through Bridged Organic Molecules

We approach the dynamics of adiabatic charge transfer through bridged triarylamine cations by a direct molecular dynamics simulation involving classical and quantum mechanical degrees of freedom. Within a simple yet chemically specific model, the quantum mechanical subsystem is described by a tight-binding Hamiltonian, which is coupled to a classical force field. From a population analysis of the quantum part, the charge transfer rate can be readily extracted, including the influence of memory effects. The direct computation of the associated thermodynamic potential establishes a close link to analytical rate concepts. The theoretical data are compared to experiments, and the limits and possible extensions of our approach are discussed.

Direct simulation of electron transfer reactions in DNA radical cations

The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighboring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the pi stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares V(2) and the energies of basepair triplets XG(+)Y and XA(+)Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15,000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, approximately 0.07 eV, while the interstrand couplings are quite different. The energies of hole states G(+) and A(+) in the stack depend on the nature of the neighboring pairs. The XG(+)Y are by 0.5 eV more stable than XA(+)Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.

Charge transfer through a protein-nano junction

We address the problem of charge transfer (CT) between a nanosized inorganic system and a protein from a theoretical and numerical perspective. The CT process is described on an atomistic level by applying an electronic Hamiltonian that takes into account the chemical bond, vibronic coupling effects, and polarization degrees of freedom. As a structurally well-characterized example, we consider a complex of C60 and its antibody. For this system, we find a novel efficient protein CT mechanism; through-space superexchange is mediated by stacked pi orbital systems. The predicted rates are comparable to those obtained for short-range electron tunneling through covalent bonds, the fastest ground-state CT process known for proteins.