Selective Oxidation of Alkylarenes to the Aromatic Ketones or Benzaldehydes with Water.

Here a palladium-catalyzed oxidation method for converting alkylarenes into the aromatic ketones or benzaldehydes with water as the only oxygen donor is reported. This C-H bond oxidation functionalization does not require other oxidants and hydrogen acceptors, and H2 is the only byproduct. The oxygen atom introduced into the products is confirmed to be from water by the MS analysis on the product of the 18O-labeled water reaction.

Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation.

Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a preinsertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection. We calculated the relative binding free energy between a noncognate nucleotide and a cognate one at a preinsertion configuration via alchemical simulations, showing that a small selection free energy or the binding free energy difference (∼3 kBT) exists between the two nucleotides. Indeed, another preinsertion configuration favored by the noncognate nucleotides was identified, which appears to be off path for further nucleotide insertion and additionally assists the nucleotide selection. By chemical master equation (CME) approach, we show that the small selection free energy at the preinsertion site along with the off-path noncognate nucleotide filtering can help substantially to reduce the error rate and to maintain the elongation rate high in the T7 RNAP transcription.

A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation.

Pyrophosphate ion (PPi) release during transcription elongation is a signature step in each nucleotide addition cycle. The kinetics and energetics of the process as well as how it proceeds with substantial conformational changes of the polymerase complex determine the mechano-chemical coupling mechanism of the transcription elongation. Here we investigated detailed dynamics of the PPi release process in a single-subunit RNA polymerase (RNAP) from bacteriophage T7, implementing all-atom molecular dynamics (MD) simulations. We obtained a jump-from-cavity kinetic model of the PPi release utilizing extensive nanosecond MD simulations. We found that the PPi release in T7 RNAP is initiated by the PPi dissociation from two catalytic aspartic acids, followed by a comparatively slow jump-from-cavity activation process. Combining with a number of microsecond long MD simulations, we also found that the activation process is hindered by charged residue associations as well as by local steric and hydrogen bond interactions. On the other hand, the activation is greatly assisted by a highly flexible lysine residue Lys472 that swings its side chain to pull PPi out. The mechanism can apply in general to single subunit RNA and DNA polymerases with similar molecular structures and conserved key residues. Remarkably, the flexible lysine or arginine residue appears to be a universal module that assists the PPi release even in multi-subunit RNAPs with charge facilitated hopping mechanisms. We also noticed that the PPi release is not tightly coupled to opening motions of an O-helix on the fingers domain of T7 RNAP according to the microsecond MD simulations. Our study thus supports the Brownian ratchet scenario of the mechano-chemical coupling in the transcription elongation of the single-subunit polymerase.

A critical residue selectively recruits nucleotides for t7 RNA polymerase transcription fidelity control.

Nucleotide selection is essential for fidelity control in gene replication and transcription. Recent work on T7 RNA polymerase suggested that a small posttranslocation free energy bias stabilizes Tyr(639) in the active site to aid nucleotide selection. However, it was not clear exactly how Tyr(639) assists the selection. Here we report a molecular-dynamics simulation study revealing atomistic detail of this critical selectivity. The study shows first that Tyr(639) blocks the active site at posttranslocation by marginally stacking to the end basepair of the DNA-RNA hybrid. The study then demonstrates that at the nucleotide preinsertion state, a cognate RNA nucleotide does not affect the local Tyr(639) stabilization, whereas a noncognate nucleotide substantially stabilizes Tyr(639) so that Tyr(639) keeps blocking the active site. As a result, further nucleotide insertion into the active site, which requires moving Tyr(639) out of the site, would be hindered for the noncognate nucleotide, but not for the cognate nucleotide. In particular, we note that water molecules assist the ribose recognition in the RNA nucleotide preinsertion, and help Tyr(639) stacking to the end basepair in the case of a DNA nucleotide. It was also seen that a base-mismatched nucleotide at preinsertion directly grabs Tyr(639) for the active site stabilization. We also find that in a mutant polymerase Y639F the strong stabilization of residue 639 in the active site cannot establish upon the DNA nucleotide preinsertion. The finding explains the reduced differentiation between ribo- and deoxyribonucleotides that has been recorded experimentally for the mutant polymerase.

Description of ionic surfactant/water system by adjusting mesoscopic parameters.

Dissipative particle dynamics simulations were utilized to simulate a model surfactant solution-air system. Amphiphilic surfactant molecules were modeled as dimers composed of a hydrophilic head and a hydrophobic tail. With a simple model, the influence of conservative interaction parameters on the surfactant's properties, including surfactant efficiency and critical micelle concentration (CMC), was investigated in the present research. It is not the surfactant total concentration, but the bulk concentration, that should be employed to achieve the right surfactant properties. It is found that the adjustment of interaction between water and head or air and tail (a(WH) or a(AT)) will result in the obvious change in surfactant efficiency. The parameter that affects CMC the most significantly is the interaction between water and tail (a(WT)). On the basis of the findings about the relationship between conservative interaction parameters and surfactant behaviors, we varied the interaction parameters and simulated a real ionic surfactant system with different tail lengths.