Machine-Learned Free Energy Surfaces for Capillary Condensation and Evaporation in Mesopores

Using molecular simulations, we study the processes of capillary condensation and capillary evaporation in model mesopores. To determine the phase transition pathway, as well as the corresponding free energy profile, we carry out enhanced sampling molecular simulations using entropy as a reaction coordinate to map the onset of order during the condensation process and of disorder during the evaporation process. The structural analysis shows the role played by intermediate states, characterized by the onset of capillary liquid bridges and bubbles. We also analyze the dependence of the free energy barrier on the pore width. Furthermore, we propose a method to build a machine learning model for the prediction of the free energy surfaces underlying capillary phase transition processes in mesopores.

Substrate Specificity for Human Histidine Methyltransferase SETD3

Histidine methyltransferase SETD3 plays an important role in human biology and diseases. Previously, we showed that SETD3 catalyzes N3-methylation of histidine 73 in β-actin (Kwiatkowski et al., 2018). Here we report integrated synthetic, biocatalytic, biostructural and computational analyses on human SETD3-catalyzed methylation of β-actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N-nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free-energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic and functional insight into β-actin histidine methylation by SETD3.

Thermodynamic approach for the understanding of the kinetics of heat effects induced by structural relaxation of metallic glasses

We present a novel approach to the understanding of heat effects induced by structural relaxation of metallic glasses. The key idea consists in the application of a general thermodynamic equation for the entropy change due to the evolution of a non-equilibrium part of a complex system. This non-equilibrium part is considered as a defect subsystem of glass and its evolution is governed by local thermoactivated rearrangements with a Gibbs free energy barrier proportional to the high-frequency shear modulus. The only assumption on the nature of the defects is that they should provide a reduction of the shear modulus – a diaelastic effect. This approach allows to determine glass entropy change upon relaxation. On this basis, the kinetics of the heat effects controlled by defect-induced structural relaxation is calculated. A very good agreement between the calculation and specially performed calorimetric and shear modulus measurements on three metallic glasses is found.

Theoretical Study on Ethylene Polymerization Catalyzed by Half-Titanocenes Bearing Different Ancillary Groups

Half-titanocenes are well known to show high activity for ethylene polymerization and good capability for copolymerization of ethylene with other olefins, and the ancillary ligands can crucially affect the catalytic performance. In this paper, the mechanisms of ethylene polymerization catalyzed by three half-metallocenes, (η5-C5Me5)TiCl2(O-2,6-iPr2C6H3) (1), (η5-C5Me5)TiCl2(N=CtBu2) (2) and [Me2Si(η5-C5Me4)(NtBu)]TiCl2 (3), have been investigated by density functional theory (DFT) method. At the initiation stage, a higher free energy barrier was determined for complex 1, probably due to the presence of electronegative O atom in phenoxy ligand. At the propagation stage, front-side insertion of the second ethylene is kinetically more favorable than back-side insertion for complexes 1 and 2, while both side insertion orientations are comparable for complex 3. The energy decomposition showed that the bridged cyclopentadienyl amide ligand could enhance the rigidity of the active species as suggested by the lowest deformation energy derived from 3. At the chain termination stage, β-H transfer was calculated to be a dominant chain termination route over β-H elimination, presumably owing to the thermodynamic perspective.

Theoretical Study on V Atom Supported on N and P-Doped Defective Graphene for Electrocatalytic Nitrogen Reduction

Ammonia (NH3) is one of the most extensively produced chemicals worldwide, and it plays an important and indispensable role in the global economy. At present NH3 is mainly produced by the traditional Haber-Bosch process operated at high pressure and temperature, which results in massive energy consumption and carbon dioxide emissions. The electrochemical nitrogen reduction reaction (NRR) can allow the production of NH3 from nitrogen and water under ambient conditions and is regarded as a sustainable alternative to the Haber–Bosch process because of its low energy consumption and limited environmental impact. In this study, using density functional theory calculations, we designed a monovacancy defective graphene (MVG) doped with various nitrogen and phosphorus atoms and a single vanadium atom (VN1–3@MVG and VP1–3@MVG) to be used as electrocatalysts. The results revealed that N- and P-doping are beneficial for N2 adsorption and activation and can effectively reduce the energy barrier of the NRR, especially for P-doping. Among the synthesized electrocatalysts, double P-doped V@MVG demonstrated the best catalytic activity with a low free energy barrier of 0.43 eV. This paper reports the development of an efficient catalyst for electrochemical NH3 synthesis and provides valuable insights on the design of electrocatalysts with high activity and stability.

An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations

Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the cis conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the cis and trans states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline cis and trans states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in cis, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in trans. The ensemble containing cis prolines also matches more closely to in vitro circular dichroism data than the all-trans ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with in vitro data.

Time-Resolved X-ray Operando Observations of Lithiation Gradients across the Cathode Matrix and Individual Oxide Particles during Fast Cycling of a Li-Ion Cell

Self-supporting three-dimensional (3D) transition metal electrodes have been considered for designing high-performance non-noble metal oxygen evolution reaction (OER) catalysts owing to their advantages such as binder-free, good mass transfer, and large specific surface area. However, the poor conductivity of ((oxy)hydr)oxides and the difficulty in adjusting their electronic structure limit their application. As an alternative strategy, instead of constituting the array electrode by the active components themselves, we herein report 3D Co(OH)2@MnO2 heterostructure decorated carbon nanoarrays grown directly on carbon paper (Co(OH)2@MnO2-CNAs). This unique structure can not only enhance electrical conductivity but also provide a larger specific surface area, and facilitate electrolyte diffusion and ion transport. The core-shell heterostructured Co(OH)2@MnO2 formed via incorporation with MnO2 facilitates the transition of CoII to CoIII in Co(OH)2 and it increases the storage of oxidative charge in the catalyst, leading to an OER activity with benchmark RuO2 and good stability. Density functional theory calculations suggest that the improved OER performance can be attributed to the formation of the heterojunction structure, resulting in the modulation of the electronic structure of Co atoms and the reduction of the free energy barrier of the rate-determining step for the OER.

Pyruvic acid, an efficient catalyst in SO₃ hydrolysis and effective clustering agent in sulfuric acid-based new particle formation

The role of pyruvic acid (PA), one of the most abundant α-keto carboxylic acids in the atmosphere, was investigated both in the SO3 hydrolysis reaction to form sulfuric acid (SA) and in SA-based aerosol particle formation using quantum chemical calculations and a cluster dynamics model. We found that the PA-catalyzed SO3 hydrolysis is a thermodynamically driven transformation process, proceeding with a negative Gibbs free energy barrier, ca. −1 kcal mol−1 at 298 K, ~6.50 kcal mol−1 lower than that in the water-catalyzed SO3 hydrolysis. Results indicated that the PA-catalyzed reaction can potentially compete with the water-catalyzed SO3 reaction in SA production, especially in dry and polluted areas, where it is found to be ~two orders of magnitude more efficient that the water-catalyzed reaction. Given the effective stabilization of the PA-catalyzed SO3 hydrolysis product as SA•PA cluster, we proceeded to examine the PA clustering efficiency in sulfuric acid-pyruvic acid-ammonia (SA-PA-NH3) system. Our thermodynamic data used in the Atmospheric Cluster Dynamics Code indicated that under relevant tropospheric temperatures and concentrations of SA (106 cm3), PA (1010 cm3) and NH3 (1011 and 5 × 1011 cm3), of the PA-containing clusters, only clusters with one PA molecule, namely (SA)2•PA•(NH3)2, can participate to the particle formation, contributing by ~100 % to the net flux to aerosol particle formation at 238 K, exclusively. At higher temperatures (258 K and 278 K), however, the net flux to the particle formation is dominated by pure SA-NH3 clusters, while PA would rather evaporate from the clusters at high temperatures and not contribute to the particle formation. The enhancing effect of PA of examined by evaluating the ratio of the ternary SA-PA-NH3 cluster formation rate to binary SA-NH3 cluster formation rate. Our results show that while the enhancement factor of PA to the particle formation rate is almost insensitive to investigated temperatures and concentrations, it can be as high as 4.7 × 102 at 238 K and [NH3] = 1.3 × 1011 molecule cm−3. This indicates that PA may actively participate in aerosol formation, only in cold regions of the troposphere and highly NH3-polluted environments. The inclusion of this mechanism in aerosol models may definitely reduce uncertainties that prevail in modeling the aerosol impact on climate.

Water cavitation from ambient to high temperatures

Predicting cavitation has proved a formidable task, particularly for water. Despite the experimental difficulty of controlling the sample purity, there is nowadays substantial consensus on the remarkable tensile strength of water, on the order of −120 MPa at ambient conditions. Recent progress significantly advanced our predictive capability which, however, still considerably depends on elaborate fitting procedures based on the input of external data. Here a self-contained model is discussed which is shown able to accurately reproduce cavitation data for water over the most extended range of temperatures for which accurate experiments are available. The computations are based on a diffuse interface model which, as only inputs, requires a reliable equation of state for the bulk free energy and the interfacial tension. A rare event technique, namely the string method, is used to evaluate the free-energy barrier as the base for determining the nucleation rate and the cavitation pressure. The data allow discussing the role of the Tolman length in determining the nucleation barrier, confirming that, when the size of the cavitation nuclei exceed the thickness of the interfacial layer, the Tolman correction effectively improves the predictions of the plain Classical Nucleation Theory.

Evidence for an N-halohistidyl Intermediate in the Catalytic Cycle of Vanadium Chloroperoxidase (VCPO) and an Artificial Enzyme derived from VCPO: A Computational Investigation

Vanadium haloperoxidases play an important catalytic role in the natural production of antibiotics which are difficult to make in the laboratory. Understanding the catalytic mechanism of these enzymes will aide in the production of artificial enzymes useful in bioengineering the synthesis of drugs and useful chemicals. However, the catalytic mechanism remains not fully understood yet. In this paper, we investigate one of the key steps of the catalytic mechanism using QM/MM. Our investigation reveals a new N-haloxy histidyl intermediate in the catalytic cycle of vanadium chloroperoxidase (VCPO). This new intermediate, in turn, yields an explanation for the known inhibition of the enzyme by substrate under acidic conditions (pH<4). Additionally, we examine the possibility of replacing V in VCPO by Nb or Ta using QM modeling. We report the new result that the Gibbs free energy barrier of several steps of the catalytic cycle are lower in the case of artificial enzymes, incorporating NbO43- or TaO43- instead of VO43-. Our results suggest that these new artificial enzymes may catalyze the oxidation of halide faster than the natural enzyme.