Fully Automated Generation of Prebiotically Relevant Reaction Networks from Optimized Nanoreactor Simulations.

The nanoreactor approach first introduced by the group of Martı́nez [Wang et al. 1044-1048] has recently attracted much attention because of its ability to accelerate the discovery of reaction pathways. Here, we provide a comprehensive study of various simulation parameters and present an alternative implementation for the reactivity-enhancing spherical constraint function, as well as for the detection of reaction events.

Exponential averaging umbrella sampling for computing the QM/MM free energy barrier of the initial step of the desuccinylation reaction catalyzed by sirtuin 5.

The computational characterization of enzymatic reactions poses a great challenge which arises from the high dimensional and often rough potential energy surfaces commonly explored by static QM/MM methods such as adiabatic mapping (AM). The present study highlights the difficulties in estimating free energy barriers exponential averaging over AM pathways. Based on our previous study [von der Esch , , 2019, , 6660-6667], where we analyzed the first reaction step of the desuccinylation reaction catalyzed by human sirtuin 5 (SIRT5) by means of QM/MM adiabatic mapping and machine learning, we use, here, umbrella sampling to compute the free energy profile of the initial reaction step.

Quantitative Comparison of Experimental and Computed IR-Spectra Extracted from Ab Initio Molecular Dynamics.

Experimentally measured infrared spectra are often compared to their computed equivalents. However, the accordance is typically characterized by visual inspection, which is prone to subjective judgment. The primary challenge for a similarity-based analysis is that the artifacts introduced by each approach are very different and, therefore, may require preprocessing steps to determine and correct impeding irregularities.

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5.

Sirtuin 5 is a class III histone deacetylase that, unlike its classification, mainly catalyzes desuccinylation and demanoylation reactions. It is an interesting drug target that we use here to test new ideas for calculating reaction pathways of large molecular systems such as enzymes. A major issue with most schemes (e.

Influence of Relativistic Effects on Bonding Modes in M(II) Dinuclear Complexes (M = Au, Ag, and Cu).

The stability and bonding in dinuclear group 11 metal complexes (M = Au, Ag, and Cu) in their +2 oxidation state has been investigated by quantum chemical methods. Two model complexes were selected as representatives of different bonding situations in the dinuclear M(II) complexes, a direct metal-metal bond between two ligand stabilized monomers and ligand-mediated bridged dimer system, making them interesting for a direct comparison and to study the influence of relativistic effects. Relativity substantially stabilizes the direct metal-metal bonded system obtaining the sequence in M-M bond stability Au > Ag > Cu.