Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations

Development of a Mg/O ReaxFF Potential to describe the Passivation Processes in Magnesium-Ion Batteries

One of the key challenges preventing the breakthrough of magnesium-ion batteries (MIB) is the formation of a passivating boundary layer at the Mg anode. To describe the initial steps of Mg anode degradation by O2 impurities, a Mg/O ReaxFF (force field for reactive systems) parameter set was developed capable of accurately modeling the bulk, surface, adsorption, and diffusion properties of metallic Mg and the salt MgO. It is shown that O2 immediately dissociates upon first contact with the Mg anode (modeled as Mg(0001), Mg(101 ‾ $\bar 1$ 0)A, and Mg(101 ‾ $\bar 1$ 1)), heating the surface to several 1000 K. The high temperature assists the further oxidation and forms a rock salt interphase intersected by several grain boundaries. Among the Mg surface terminations, Mg(101 ‾ $\bar 1$ 0)A is the most reactive, forming an MgO layer with a thickness of up to 25 Å. The trained force field can be used to model the ongoing reactions in Mg-air batteries but also to study the oxidation of magnesium metal in general.

Application of Q2MM to predictions in stereoselective synthesis

Quantum-Guided Molecular Mechanics (Q2MM) can be used to derive transition state force fields (TSFFs) that allow the fast and accurate predictions of stereoselectivity for a wide range of catalytic enantioselective reactions. The basic ideas behind the derivation of TSFFs using Q2MM are discussed and the steps involved in obtaining a TSFF using the Q2MM code, publically available at github.com/q2mm, are shown. The applicability for a range of reactions, including several non-standard applications of Q2MM, is demonstrated. Future developments of the method are also discussed.

The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube

As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon-based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress-strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress-strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed.

Tribochemical mechanism of amorphous silica asperities in aqueous environment: a reactive molecular dynamics study

Reactive molecular dynamics (ReaxFF) simulations are used to explore the atomic-level tribochemical mechanism of amorphous silica (a-SiO2) in a nanoscale, single-asperity contact in an aqueous environment. These sliding simulations are performed in both a phosphoric acid solution and in pure water under different normal pressures. The results show that tribochemical processes have profound consequences on tribological performance. Water molecules could help avoid direct adhesive interaction between a-SiO2 surfaces in pure water under low normal load. However, formation and rupture of interfacial siloxane bonds are obviously observed under higher normal load. In phosphoric acid solution, polymerization of phosphoric acid molecules occurs, yielding oligomers under lower load, and tribochemical reactions between the molecules and the sliding surfaces could enhance wear under higher load. The bridging oxygen atoms in silica play an important role in the formation of interfacial covalent bonds, and hydrogen is found to have a weakening effect on these bonds, resulting in the rupture during shear-related loading. This work sheds light on tribochemical reactions as a mechanism for lubrication and wear in water-based or other tribological systems.

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II

An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.

Stability and metastability of clusters in a reactive atmosphere: theoretical evidence for unexpected stoichiometries of MgMOx

By applying a genetic algorithm and ab initio atomistic thermodynamics, we identify the stable and metastable compositions and structures of MgMOx clusters at realistic temperatures and oxygen pressures. We find that small clusters (M≲5) are in thermodynamic equilibrium when x>M. The nonstoichiometric clusters exhibit peculiar magnetic behavior, suggesting the possibility of tuning magnetic properties by changing environmental pressure and temperature conditions. Furthermore, we show that density-functional theory with a hybrid exchange-correlation functional is needed for predicting accurate phase diagrams of metal-oxide clusters. Neither a (sophisticated) force field nor density-functional theory with (semi)local exchange-correlation functionals is sufficient for even a qualitative prediction.

Reversible intercalation of hexagonal boron nitride with Brønsted acids

Hexagonal boron nitride (h-BN) is an insulating compound that is structurally similar to graphite. Like graphene, single sheets of BN are atomically flat, and they are of current interest in few-layer hybrid devices, such as transistors and capacitors, that contain insulating components. While graphite and other layered compounds can be intercalated by redox reactions and then converted chemically to suspensions of single sheets, insulating BN is not susceptible to oxidative intercalation except by extremely strong oxidizing agents. We report that stage-1 intercalation compounds can be formed by simple thermal drying of h-BN in Brønsted acids H2SO4, H3PO4, and HClO4. X-ray photoelectron and vibrational spectra, as well as electronic structure and molecular dynamics calculations, demonstrate that noncovalent interactions of these oxyacids with the basic N atoms of the sheets drive the intercalation process.

Control of transcriptional fidelity by active center tuning as derived from RNA polymerase endonuclease reaction

Precise transcription by cellular RNA polymerase requires the efficient removal of noncognate nucleotide residues that are occasionally incorporated. Mis-incorporation causes the transcription elongation complex to backtrack, releasing a single strand 3'-RNA segment bearing a noncognate residue, which is hydrolyzed by the active center that carries two Mg(2+) ions. However, in most x-ray structures only one Mg(2+) is present. This Mg(2+) is tightly bound to the active center aspartates, creating an inactive stable state. The first residue of the single strand RNA segment in the backtracked transcription elongation complex strongly promotes transcript hydrolytic cleavage by establishing a network of interactions that force a shift of stably bound Mg(2+) to release some of its aspartate coordination valences for binding to the second Mg(2+) thus enabling catalysis. Such a rearrangement that we call active center tuning (ACT) occurs when all recognition contacts of the active center-bound RNA segment are established and verified by tolerance to stress. Transcription factor Gre builds on the ACT mechanism in the same reaction by increasing the retention of the second Mg(2+) and by activating the attacking water, causing 3000-4000-fold reaction acceleration and strongly reinforcing proofreading. The unified mechanism for RNA synthesis and degradation by RNA polymerase predicts that ACT also executes NTP selection thereby contributing to high transcription fidelity.

Basic mechanism of transcription by RNA polymerase II

RNA polymerase II-like enzymes carry out transcription of genomes in Eukaryota, Archaea, and some viruses. They also exhibit fundamental similarity to RNA polymerases from bacteria, chloroplasts, and mitochondria. In this review we take an inventory of recent studies illuminating different steps of basic transcription mechanism, likely common for most multi-subunit RNA polymerases. Through the amalgamation of structural and computational chemistry data we attempt to highlight the most feasible reaction pathway for the two-metal nucleotidyl transfer mechanism, and to evaluate the way catalysis can be linked to translocation in the mechano-chemical cycle catalyzed by RNA polymerase II. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop

Tagetitoxin (Tgt) inhibits multisubunit chloroplast, bacterial, and some eukaryotic RNA polymerases (RNAPs). A crystallographic structure of Tgt bound to bacterial RNAP apoenzyme shows that Tgt binds near the active site but does not explain why Tgt acts only at certain sites. To understand the Tgt mechanism, we constructed a structural model of Tgt bound to the transcription elongation complex. In this model, Tgt interacts with the β' subunit trigger loop (TL), stabilizing it in an inactive conformation. We show that (i) substitutions of the Arg residue of TL contacted by Tgt confer resistance to inhibitor; (ii) Tgt inhibits RNAP translocation, which requires TL movements; and (iii) paused complexes and a "slow" enzyme, in which the TL likely folds into an altered conformation, are resistant to Tgt. Our studies highlight the role of TL as a target through which accessory proteins and antibiotics can alter the elongation complex dynamics.

Reactive molecular dynamics study on the first steps of DNA damage by free hydroxyl radicals

We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen abstraction as well as formation of carbonyl and hydroxyl groups in the sugar moiety that create holes in the sugar rings. These holes grow up slowly between DNA bases and DNA backbone, and the damage collectively propagates to a DNA single and double strand break.

Exploring the molecular origin of the high selectivity of multisubunit RNA polymerases by stochastic kinetic models

RNA polymerases are molecular machines of great fidelity, which can recognize matched NTPs from unmatched NTPs and 2'-dNTPs. We investigated by a stochastic simulation algorithm the whole nucleotide addition cycle based on an event-driven model. This model allows us to examine possible molecular origins of the high fidelity of RNA polymerases. For unmatched NTP selectivity, the conclusions drawn from simulated elongation rates corroborate those derived from structural analysis. The presence of two conformations (Esite and pre-insertion site) for the incoming nucleotide before the polymerization reaction is sufficient to allow selectivity. Concerning sugar selectivity, our results indicate that selectivity is only achievable if slow chemical reactions occur for 2'-dNTP. These results can be used to understand recent experimental observations.