Accelerated Lignocellulosic Molecule Adsorption Structure Determination.

Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules ß-d-xylose and 1,4-ß-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.

Elucidation of protein-ligand interactions by multiple trajectory analysis methods.

The identification of interaction between protein and ligand including binding positions and strength plays a critical role in drug discovery. Molecular docking and molecular dynamics (MD) techniques have been widely applied to predict binding positions and binding affinity. However, there are few works that describe the systematic exploration of the MD trajectory evolution in this context, potentially leaving out important information. To address the problem, we build a framework, Moira (molecular dynamics trajectory analysis), which enables automating the whole process ranging from docking, MD simulations and various analyses as well as visualizations. We utilized Moira to analyze 400 MD simulations in terms of their geometric features (root mean square deviation and protein-ligand interaction profiler) and energetics (molecular mechanics Poisson-Boltzmann surface area) for these trajectories. Finally, we demonstrate the performance of different analysis techniques in distinguishing native poses among four poses.

The unimolecular dissociation of magnesium chloride squarate (ClMgC4O4-) and reductive cyclooligomerisation of CO on magnesium.

In this paper, we present an investigation of the unimolecular dissociation of an anionic magnesium chloride squarate complex, ClMgC4O4- using mass spectrometry supported by theoretical reaction models based on quantum chemical calculations. Sequential decarbonylation is the main fragmentation pathway leading to the deltate and ethenedione complexes, ClMgC3O3- and ClMgC2O2-, and MgCl--yet the monomer, ClMgCO-, is not observed. Calculations using the G4 composite method show that the latter is unstable with respect to further dissociation. The implications for the reverse reaction sequence, cyclooligomerisation of CO on MgCl-, are discussed in detail and also compared with recent results from synthetic efforts in finding benign and efficient metal catalysed pathways to squaric acid from CO by reduction. It appears that the first step in these reactions, the formation of the first C-C bond by coupling of two CO molecules on MgCl-, is the most critical. The role of electron transfer in step-by-step stabilising the nascent CnOn centre is highlighted.

Characterization of the alkali metal oxalates (MC2O4-) and their formation by CO2 reduction via the alkali metal carbonites (MCO2-).

The reduction of carbon dioxide to oxalate has been studied by experimental Collisionally Induced Dissociation (CID) and vibrational characterization of the alkali metal oxalates, supplemented by theoretical electronic structure calculations. The critical step in the reductive process is the coordination of CO2 to an alkali metal anion, forming a metal carbonite MCO2- able to subsequently receive a second CO2 molecule. While the energetic demand for these reactions is generally low, we find that the degree of activation of CO2 in terms of charge transfer and transition state energies is the highest for lithium and systematically decreases down the group (M = Li-Cs). This is correlated to the strength of the binding interaction between the alkali metal and CO2, which can be related to the structure of the oxalate moiety within the product metal complexes evolving from a planar to a staggered conformer with increasing atomic number of the interacting metal. Similar structural changes are observed for crystalline alkali metal oxalates, although the C2O42- moiety is in general more planar in these, a fact that is attributed to the increased number of interacting alkali metal cations compared to the gas-phase ions.

Unimolecular Dissociation of Hydrogen Squarate (HC4O4-) and the Squarate Radical Anion (C4O4•-) in the Gas Phase and the Relationship to CO Cyclooligomerization.

The unimolecular dissociation of hydrogen squarate and the squarate radical anion has been studied by electrospray ionization mass spectrometry (including collisionally induced dissociation) and quantum chemical calculations, providing consistent reaction models. In both cases, consecutive decarbonylations are observed as the dominating fragmentations. The reverse of these reactions corresponds to the successive cyclooligomerization of CO, which constitutes the most atom-efficient route to the cyclic oxocarbons. The reaction models indicate moderate barriers for CO addition to HCnOn- and CnOn•-, respectively, being larger for the former than for the latter. Cyclooligomerization leading to a neutral product is endothermic, while the analogous one-electron reductive coupling is exothermic. The analysis shows that the addition of an electron is essential for cyclooligomerization to give the cyclic four-CO squarate structure.

Unimolecular dissociation of anions derived from succinic acid (H2Su) in the gas phase: HSu- and ClMgSu-. Relationship to CO2 fixation.

Electrospray ionization of mixtures of succinic acid (here denoted H2Su) and magnesium chloride in water/methanol give rise to ions of the type ESu- (E = H or ClMg). The unimolecular dissociation of these ions was studied by collisionally induced dissociation mass spectrometry and interpreted by quantum chemical calculations (density functional theory and the composite Gaussian-4 method) of relevant parts of the potential energy surfaces. The major dissociation pathways from HSu- were seen to be dehydration and decarboxylation, while ClMgSu- mainly undergoes decarboxylation. The latter reaction proceeds without barrier for the reverse reaction; addition of CO2 to a Grignard type structure ClMg(CH2CH2CO2)-. In contrast, addition of CO2 to the analogous H(CH2CH2CO2)- ion has a substantial barrier. Dehydration of HSu- gives rise to deprotonated succinic anhydride via a transition state for the key intramolecular proton transfer having an entropically favorable seven-member ring structure. The succinate systems studied here are compared to the previously reported analogous maleate systems, providing further insight to the structure-reactivity relationship.