What Singles Out the G[8-5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the CS atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be similar to 12.4 kcal/mol, which is similar to 3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, 3., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc. 134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (similar to 10.5 kcal/mol). The order of reactivity in DNA (T-center dot > mC(center dot) > C-center dot) is reversed compared to that in the reacting subsystems in the gas phase (C-center dot > mC(center dot) > T-center dot), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

John Maddocks, Marco Pasi, Daiva Petkeviciute

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.

Oxford University Press (OUP)2019

Alignment of energy levels in amorphous oxides and at semiconductor-water interfaces

Zhendong Guo

We conduct a detailed investigation of defects in two representative amorphous oxides: amorphous Al2O3 (am-Al2O3) and TiO2 (am-TiO2), by combining ab initio molecular dynamics (MD) simulations and hybrid functional calculations. Our results indicate that oxygen vacancies and interstitials occur neither in am-Al2O3 nor in am-TiO2 due to structural rearrangements which assimilate the defect structure, and that the injection of extra holes can lead to the formation of O-O peroxy linkages. In am-Al2O3, hydrogen is found to be amphoteric. Based on localized Wannier functions, we identify the nominal charge state and the composition of the defect core units related to C and N impurities in am-Al2O3, which are found to depend on the total charge set in the simulation cell. Through the adopted electron counting rule, we assess that carbon and nitrogen impurities are only found in neutral and in singly positive charge states, respectively, indicating that none of them gives charge transition levels in am-Al2O3. In addition, those defect core units are shown to incorporate a varying number of oxygen atoms, by which their formation energy is dependent on the oxygen chemical potential. In addition, we propose an exchange mechanism for hole transport in am-TiO2 that relies on the simultaneous breaking and forming of O-O peroxy linkages that share one O atom. Through the use of nudged-elastic-band calculations, a hopping path as long as 1.2 nm with barriers of 0.3-0.5 eV is demonstrated, suggesting that hole diffusion through O-O peroxy linkages is viable in am-TiO2. In this work, we also determine the band alignment between various semiconductors and liquid water by combining MD simulations of atomistic interface models, electronic-structure calculations at the hybrid-functional and GW levels, and a computational standard hydrogen electrode (SHE). Our study comprises GaAs, GaP, GaN, CdS, ZnO, SnO2, rutile and anatase TiO2. For each semiconductor, we generate atomistic interface models with liquid water at the pH corresponding to the point of zero charge. The MD simulations are started from initial configurations, in which the water molecules are either molecularly (m) or dissociatively (d) adsorbed on the semiconductor surface. The calculated band offsets are found to be strongly influenced by the adsorption mode at the semiconductor-water interface, leading to differences larger than 1 eV between m and d models of the same semiconductor. We then assess the accuracy of various ab initio electronic-structure schemes in determining the band alignment. In the last part, we try to evaluate photocatalysts for water-splitting by considering the surface coverage and the energy alignment. We determine surface concentrations of water molecules, protons, and hydroxyl ions adsorbed at the semiconductor-water interfaces mentioned above as a function of pH. This is achieved through the calculation of the acidity constants at the surface sites, which are derived from ab initio MD simulations and a grand-canonical formulation of adsorbates. It is finally shown how the potential of a semiconductor material as photocatalysts for water splitting can be inferred by combining the nature of the surface coverage and the alignment of the band edges to the relevant redox levels.

EPFL2019

Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials

Luc Sébastien Bondaz, Rohit Karnik

Nanoporous single-layer graphene is promising as an ideal membrane because of its extreme thinness, chemical resistance, and mechanical strength, provided that selective nanopores are successfully incorporated. However, screening and understanding the transport characteristics of the large number of possible pores in graphene are limited by the high computational requirements of molecular dynamics (MD) simulations and the difficulty in experimentally characterizing pores of known structures. MD simulations cannot readily simulate the large number of pores that are encountered in actual membranes to predict transport, and given the huge variety of possible pores, it is hard to narrow down which pores to simulate. Here, we report alternative routes to rapidly screen molecules and nanopores with negligible computational requirement to shortlist selective nanopore candidates. Through the 3D representation and visualization of the pores' and molecules' atoms with their van der Waals radii using open-source software, we could identify suitable C-passivated nanopores for both gas- and liquid-phase separation while accounting for the pore and molecule shapes. The method was validated by simulations reported in the literature and was applied to study the mass transport behavior across a given distribution of nanopores. We also designed a second method that accounts for Lennard-Jones and electrostatic interactions between atoms to screen selective non-C-passivated nanopores for gas separations. Overall, these visualization methods can reduce the computational requirements for pore screening and speed up selective pore identification for subsequent detailed MD simulations and guide the experimental design and interpretation of transport measurements in nanoporous atomically thin membranes.