Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA.

A double proton transfer reaction in a guanine-cytosine (GC) base pair has been proposed as a possible mechanism for rare tautomer (G*C*) formation and thus a source of spontaneous mutations. We analyze this system with free energy calculations based on extensive Quantum Mechanics/Molecular Mechanics simulations to properly consider the influence of the DNA biomolecular environment. We find that, although the G*C* rare tautomer is metastable in the gas phase, it is completely unstable in the conditions found in cells. Thus, our calculations show that a double proton reaction cannot be the source of spontaneous point mutations. We have also analyzed the intrabase H transfer reactions in guanine. Our results show that the DNA environment gives rise to a large free energy difference between the rare and canonical tautomers. These results show the key role of the DNA biological environment for the stability of the genetic code.

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

Ultrafast Atomic Diffusion Inducing a Reversible (2sqrt[3]×2sqrt[3])R30°â†”(sqrt[3]×sqrt[3])R30° Transition on Sn/Si(111)∶B.

Dynamical phase transitions are a challenge to identify experimentally and describe theoretically. Here, we study a new reconstruction of Sn on silicon and observe a reversible transition where the surface unit cell divides its area by a factor of 4 at 250 °C. This phase transition is explained by the 24-fold degeneracy of the ground state and a novel diffusive mechanism, where four Sn atoms arranged in a snakelike cluster wiggle at the surface exploring collectively the different quantum mechanical ground states.

Metallization of the potassium overlayer on the ß-SiC(100) c(4 × 2) surface.

We present new data on the potassium-induced semiconducting to metallic transition of the silicon-terminated ß-SiC(100) c(4 × 2) surface, resulting from density functional theory simulations. We have analysed many different SiC(100)-K surface topologies, corresponding to K coverages ranging from 0.08 to 1.25 monolayers (ML), paying special attention to the 2/3 ML and 1 ML cases where a metal-insulator transition has been reported to occur. We find that the SiC(100)-K surface is metallic in all the cases. In spite of that, the potassium layer shows a very low density of states in the semiconductor gap up to potassium coverages of ~1 ML, beyond which the potassium layer undergoes a transition to metallic behaviour, explaining the experimental observation. We propose a new atomic model for the surface reconstruction of the 1 ML case which is lower in total energy than the previously suggested model based on linear potassium chains.

Weak dimers and soft phonons on the ß-SiC(100) surface.

We study the ß-SiC(100) [Formula: see text] reversible phase transition, using first-principles molecular dynamics simulations to search for the ground state atomic structure as well as to investigate the dynamics of this surface. We find that this surface consists of weakly bonded asymmetric Si dimers that exhibit a complex atomic motion, associated with a surface soft phonon. This soft phonon is strongly coupled to the electrons in dangling bond states close to the Fermi level, explaining the observed insulator-metal transition. We identify the dynamical processes responsible for the phase transition and predict that this surface should undergo another reversible phase transition at low T.