Minimum Energy Pathways Research Articles

Hydrogen adsorption and diffusion through a two dimensional sheet of lithium: a first principles study.

Two-dimensional (2D) materials have shown promise as highly selective, ultrathin membranes to transport ions, and atomic and subatomic particles. They have also been regarded as potential hydrogen storage candidates due to their chemical stability and high specific surface area. However, most of these studies have been carried out with semiconducting 2D materials. With recent explorations towards the existence and stability of 2D metals, we explore the hydrogen adsorption and diffusion through a 2D metallic sheet of lithium. We report that in the lowest energy metallic configuration, the sheet is predicted to crystallize in a highly buckled honeycomb structure. We calculate the adsorption energy for the diffusion of hydrogen on various high symmetry sites in the lattice, and find that adsorption is energetically favoured. We study the minimum energy pathways for diffusion through the sheet and find that the lowest energy barriers exist for tunneling through the honeycomb ring. Our results would be of direct technological relevance to the applications of 2D metallic nanostructures as membranes for selective transport or towards storage.

Electrocatalytic study of the hydrogen evolution reaction on MoS2/BP and MoSSe/BP in acidic media.

Molecular hydrogen (H2) production by the electrochemical hydrogen evolution reaction (HER) is being actively explored for non-precious metal-based electrocatalysts that are earth-abundant and low cost like MoS2. Although it is acid-stable, its applicability is limited by catalytically inactive basal planes, poor electrical transport and inefficient charge transfer at the interface. Therefore, the present work examines its bilayer van der Waals heterostructure (vdW HTS). The second constituent monolayer boron phosphide (BP) is advantageous as an electrode material owing to its chemical stability in both oxygen and water environments. Here, we have performed first-principles based calculations under the framework of density functional theory (DFT) for the HER in an electrochemical double layer model with the BP monolayer, MoS2/BP and MoSSe/BP vdW HTSs. The climbing image nudged elastic band method (CI-NEB) has been employed to determine the minimum energy pathways for Tafel and Heyrovsky reactions. The calculations reveal that the Tafel reaction shows no reaction barrier. Thereafter, for the Heyrovsky reaction, we obtained a low reaction barrier in the vdW HTSs as compared to that in the BP monolayer. Subsequently, we have observed no significant difference in the reaction profile of MoS2/BP and MoSSe/BP vdW HTSs in the case of 2 × 2 supercell configuration. However, in the case of 3 × 3 and 4 × 4 configurations, MoSSe/BP shows a feasible Heyrovsky reaction with no reaction barrier. The coverages with 1/4H+ concentration (conc.) deduced high coverage with low conc. and low coverage with high conc. to be apt for the HER via the Heyrovsky reaction path. Finally, on observing the activation barrier of the Heyrovsky pathway along with that of second H adsorption at the surface, the Heyrovsky path is expected to be favoured.

Surfactant in a Polyol-CO2 Mixture: Insights from a Classical Density Functional Theory Study.

Silicone-polyether (SPE) surfactants, made of a polydimethyl-siloxane (PDMS) backbone and polyether branches, are commonly used as additives in the production of polymeric foams with improved properties. A key step in the production of polymeric foams is the nucleation of gas bubbles in the polymer matrix upon supersaturation of dissolved gas. However, the role of SPE surfactants in the nucleation of gas bubbles is not well understood. In this study, we use classical density functional theory to investigate the effect of an SPE surfactant on the nucleation of CO2 bubbles in a polyol foam formulation. We find that the addition of an SPE surfactant leads to a ∼3-fold decrease in the polyol-CO2 interfacial tension at the surfactant's critical micelle concentration. Additionally, the surfactant is found to reduce the free energy barrier and affect the minimum free energy pathway (MFEP) associated with CO2 bubble nucleation. In the absence of a surfactant, a CO2-rich bubble nucleates from a homogeneous CO2-supersaturated polyol solution by following an MFEP characterized by a single nucleation barrier. Adding a surfactant results in a two-step nucleation process with reduced free energy barriers. The first barrier corresponds to the formation of a spherical aggregate with a liquid-like CO2 core. This spherical aggregate then grows into a CO2-rich bubble (spherical aggregate with a vapor-like CO2 core) of a critical size representing the second barrier. We hypothesize that the stronger affinity of CO2 for PDMS (than polyether) stabilizes the spherical aggregate with the liquid-like CO2 core, leading to a lower free energy barrier for CO2 bubble nucleation. Stabilization of such an aggregate during the early stages of the nucleation may lead to foams with more, smaller bubbles, which can improve their microstrustural features and insulating abilities.

Molecular adsorption of the NCO, CNO and CON isomers on the Rh(001) surface : A standard DFT and DFT+[formula omitted] calculations

The adsorption and dissociation of the NCO, CNO and CON isomeric molecules on Rh (001)-(3x3) are investigated using the standard density functional theory (DFT) and DFT with Hubbard U, i.e., DFT+U methods. The generalized gradient approximation (GGA) is used as the exchange–correlation functional. Also, three possible adsorption sites, which are hollow (H), bridge (B) and top (T) as well as two orientations, i.e., vertical and tilted, of the molecules on the Rh surface have been considered. We found that of the three isomers, the CNO molecule adsorbed at the hollow site of the Rh surface via its C atom end is the most stable for both methods. However, the inclusion of U parameter to GGA leads to the reduction in energies and slight changes in the relaxed adsorption geometries. Also, with the aid of nudged elastic band calculation (NEB), we study the minimum energy pathway (MEP) for dissociation of the CNO molecule into CN and O fragments. We obtain an activation barrier to the dissociation, Ea, of 0.97 eV with an enthalpy change ΔH = −1.25 eV. This dissociation process is found to be exothermic. Furthermore, the projected density of states (PDOS) calculations performed using the atomic structures corresponding to initial (IS), transition (TS), and the final states (FS) of the CNO dissociation process MEP show significant reduction and shifting of N-2p and O-2p states toward higher energies, as well as vanishing N-2p states. This reduction and vanishing of orbital states evidence the weakening and eventual breaking of NO bond of CNO, which eventually led to the dissociation of the CNO molecule. This is further underscored by the total electronic density plot which shows a gradual decrease and eventual vanishing of charge density between the CN and O species as the dissociation process progresses.

800 QM/MM minimum energy pathway conformations for the deacylation reactions of KPC-2/Imipenem

800 QM/MM minimum energy pathway conformations for the deacylation reactions of KPC-2/Imipenem

Ethanol exchange between two graphene surfaces in nanoconfined aqueous solution: Rate and mechanism.

We observe, by computer simulations, a remarkable long-distance, rare, but repetitive, exchange of ethanol molecules between two parallel graphene surfaces in nanoconfined, aqueous, ethanol solutions. We compute the rate of exchange as a function of the separation (d) between the two surfaces. We discover that the initiating (or, the launching) step in this exchange is the attainment of an instantaneous orientation of the carbon-oxygen bond vector relative to the graphene surface. This observation led us to construct a two-dimensional free energy surface for this exchange, with respect to two order parameters, namely, (i) the perpendicular distance of ethanol molecule from the graphene surfaces, z, and (ii) the orientation of the O-C bond vector, θ, of the tagged ethanol molecule. For d = 3nm, the rate of exchange is found to be 0.44ns-1 for the force field used. We also vary the force field and determine the sensitivity of the rate. From the free energy landscape, one could determine the minimum energy pathway. We use both, the transition state theory and Kramers' theory, to calculate the rate. The calculated rate agrees well with the simulated value as mentioned above. We find that the rate of exchange phenomenon is sensitive to the interaction strength of graphene and the hydrophobic group of ethanol. The free energy landscape exchange shows dependence on the distance separation of the two hydrophobic surfaces and reveals interesting features.

Estimates of Quantum Tunneling Effects for Hydrogen Diffusion in PuO2

We detail the estimation of activation energies and quantum nuclear vibrational tunneling effects for hydrogen diffusion in PuO2 based on Density Functional Theory calculations and a quantum double well approximation. We find that results are relatively insensitive to choice of exchange correlation functional. In addition, the representation of spin in the system and use of an extended Hubbard U correction has only a small effect on hydrogen point defect formation energies when the PuO2 lattice is held fixed at the experimental density. We then compute approximate activation energies for transitions between hydrogen interstitial sites seeded by a semi-empirical quantum model and determine the quantum tunneling enhancement relative to classical kinetic rates. Our model indicates that diffusion rates in H/PuO2 systems could be enhanced by more than one order of magnitude at ambient conditions and that these effects persist at high temperature. The method we propose here can be used as a fast screening tool for assessing possible quantum nuclear vibrational effects in any number of condensed phase materials and surfaces, where hydrogen hopping tends to follow well defined minimum energy pathways.

Multi-targeted fluorescent probes for detection of Zn(II) and Cu(II) ions based on ESIPT mechanism

With the rapid development of industry, it is pretty critical to detect the heavy metals. Recently, the 2-(2-hydroxyphenyl) benzothiazole derivatives with different numbers of rotatable phenyl m (m = 1,2,3) fluorescent probes HLm were synthesized. However, the theoretical analysis of the mechanism was still missing. In this work, we have systematically researched the mechanisms of excited state intramolecular proton transfer (ESIPT) and the detection of Cu(II), Zn(II) ions for the hydrogen-bond system HLm though quantum chemistry methods. By bond parameters and the minimum energy pathways analyses, the proton of this system was probed directly transfer without barrier. Bond parameters, real space function at bond critical point, the frontier molecular orbital, electron spectra and orbital interaction diagram were carried to elucidate response to Cu(II), Zn(II) ions. In addition, comparing the Gibbs free energy variation of the complexation reaction between fluorescent probes and ions, it can be proved that the number of rotatable benzene rings affects the response ability of the probe to target ions.

800 QM/MM minimum energy pathway conformations for the deacylation reactions of KPC-2/Imipenem

800 QM/MM minimum energy pathway conformations for the deacylation reactions of KPC-2/Imipenem

Modeling pyranose ring pucker in carbohydrates using machine learning and semi-empirical quantum chemical methods.

Pyranose ring pucker is a key coordinate governing the structure, interactions and reactivity of carbohydrates. We assess the ability of the machine learning potentials, ANI-1ccx and ANI-2x, and the GFN2-xTB semiempirical quantum chemical method, to model ring pucker conformers of five monosaccharides and oxane in the gas phase. Relative to coupled-cluster quantum mechanical calculations, we find that ANI-1ccx most accurately reproduces the ring pucker energy landscape for these molecules, with a correlation coefficient r2 of 0.83. This correlation in relative energies lowers to values of 0.70 for ANI-2x and 0.60 for GFN2-xTB. The ANI-1ccx also provides the most accurate estimate of the energetics of the 4 C1 -to-1 C4 minimum energy pathway for the six molecules. All three models reproduce chair more accurately than non-chair geometries. Analysis of small model molecules suggests that the ANI-1ccx model favors puckers with equatorial hydrogen bonding substituents; that ANI-2x and GFN2-xTB models overstabilize conformers with axially oriented groups; and that the endo-anomeric effect is overestimated by the machine learning models and underestimated via the GFN2-xTB method. While the pucker conformers considered in this study correspond to a gas phase environment, the accuracy and computational efficiency of the ANI-1ccx approach in modeling ring pucker in vacuo provides a promising basis for future evaluation and application to condensed phase environments.

Structure, Stability, and Electronic Properties of Boron Suboxide: A Density Functional Theory Study

Boron suboxide (B6O) is a boron-rich compound derived from the α-rhombohedral boron lattice with extreme hardness and unusual semiconducting properties. In this work, density functional theory (DFT) was used to show that unit cell volume, mechanical strength, band gaps, and thermodynamic stabilities of B6O were influenced by the interstitial elements and point defects at the icosahedral sites. While the hexagonal unit cell volume (HUCV) varies with interstitial occupancy, it is the icosahedral defect that weakens the intrinsic bulk modulus of B6O. Using the hybrid HSE functional, we confirmed that the perfect B6O bulk is a p-type semiconductor with a direct band gap of 2.8 eV. Furthermore, by screening α-boron compounds systematically, we found that a simple octet rule may offer a consistent explanation for the variations in the computed electronic structures. The formation free energies calculated over a wide range of temperatures (0–2500 K) and pressures (0–80 GPa) predict that formations of interstitial defects become favorable only at higher temperatures (ca. 1800 K) in bulk B6O lattices. The nudged elastic band (NEB) method was employed to identify the minimum energy pathways for the diffusions of dislocated B and O atoms. The diffusion of icosahedral B atoms has an energy barrier of 0.16 eV. More complex B diffusion paths involving the reorganization of icosahedral boron atoms incur higher barriers (>1 eV). In contrast, the diffusion of interstitial O atoms is facile with a barrier of 0.4 eV. Lastly, successive O insertions into the α-B lattice were performed using DFT to generate a basic understanding of the oxidation process. These calculations provide fundamental atomistic insights into the growth of B6O crystals and control of their point defects.

Adsorption and diffusion properties of calcium ions at the van der Waals interface of NbSe2-graphene 2D heterostructure for multivalent battery applications: density functional theory calculations

Multivalent-ion batteries such as calcium-ion batteries show promise as a high-density alternative to lithium-ion batteries which currently dominate the portable electronics market. In this work, the adsorption and diffusion properties of calcium ion at the van der Waals (vdW) interface of the 2D heterostructure formed by vertically stacking NbSe2 monolayer and graphene were investigated via density functional theory (DFT) calculations. Results showed that calcium can be effectively adsorbed on the vdW interface of the 2D heterostructure, with the binding energy of most stable site at −2.77 eV, much higher than most metal ions’ binding on pristine graphene. Thus, the NbSe2-graphene 2D heterostructure reinforced the binding of calcium ions at the interface. It is revealed that due to the random stacking nature of NbSe2 and graphene, a multi-path minimum energy pathways were identified at the van de Waals region, with relatively low diffusion barriers of around 0.20–0.50 eV. These indicate the capabilities of the 2D vdW heterostructure for fast multivalent ionic mobility and charge-discharge rate, while maintaining strong binding at the vdW interface. The results reveal NbSe2-graphene 2D vdW heterostructure’s potential as a promising anode material for multivalent battery applications.

Impact of Side-Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy-Bithiophene Semiconductors.

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.

Visualization of electron density changes along chemical reaction pathways

We propose a simple procedure for visualising the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity S N 2, Claisen rearrangement, Diels-Alder reaction, [ 3 + 2 ] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed N 2 O fragmentation, where the N–O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces.

Theoretical investigation on two-dimensional conjugated aromatic polymer membranes for high-efficiency hydrogen separation: The effects of pore size and interaction

Based on two-dimensional conjugated aromatic polymer (2D-CAP), CAP-1S/CAP-1P monolayers were designed by substituting N with S/P atoms for H2 purification. By using MD and DFT approaches, the H2 purification performance and separation mechanisms of CAP-1S/CAP-1P membranes were investigated. Results showed that ultrahigh H2 permeances of 3.546 × 10−5 and 2.593 × 10−4 mol m−2 s−1 Pa−1 were obtained in CAP-1S/CAP-1P, which were almost 104–105 times larger than the industrially acceptable standard. The selectivities of H2 over CO2/CO/CH4/N2 ranged from 5.719 × 1018 to 3.683 × 1039 in CAP-1S and 4.554 × 1013 to 2.153 × 1033 in CAP-1P. From a statistic viewpoint, the CAP-1S/CAP-1P membranes exhibited complete selectivities of H2 over CO2/CO/CH4/N2. The cohesive energies confirmed the high stabilities of CAP-1S/CAP-1P membranes. The minimum energy pathways, energy profiles, electron density, and charge density difference were analyzed to illustrate the significant impact of precise pore size on the H2 separation performance. From a statistic mechanics view, the interaction between gases and CAP-1S/CAP-1P membranes indicated that the long-range Coulomb interactions dominated the gas diffusion processes. Results of this work highlighted CAP-1P as a promising H2 separation membrane and elucidated the promotion mechanism by fine-tunning pore size and interaction between gases and membranes to balance the H2 permeance and selectivity jointly.

Graph-learning guided mechanistic insights into imipenem hydrolysis in GES carbapenemases

Pathogen resistance to carbapenem antibiotics compromises effective treatments of superbug infections. One major source of carbapenem resistance is the bacterial production of carbapenemases which effectively hydrolyze carbapenem drugs. In this computational study, the deacylation reaction of imipenem (IPM) by GES-5 carbapenemases (GES) is modeled to unravel the mechanistic factors that facilitate carbapenem resistance. Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are applied to sample the GES/IPM deacylation barriers on the minimum energy pathways (MEPs). In light of the recent emergence of graph-based deep-learning techniques, we construct graph representations of the GES/IPM active site. An edge-conditioned graph convolutional neural network (ECGCNN) is trained on the acyl-enzyme conformational graphs to learn the underlying correlations between the GES/IPM conformations and the deacylation barriers. A perturbative approach is proposed to interpret the latent representations from the graph-learning (GL) model and extract essential mechanistic understanding with atomistic detail. In general, our study combining QM/MM MEPs calculations and GL models explains mechanistic landscapes underlying the IPM resistance driven by GES carbapenemases. We also demonstrate that GL methods could effectively assist the post-analysis of QM/MM calculations whose data span high dimensionality and large sample-size.

Magnetization reversal across multiple serial barriers in a single Fe3O4 nanoparticle

Depinning of nanoscale magnetic textures, such as domain walls, vortices and skyrmions, is of paramount importance for magnetic storage and information processing. We measure time-resolved magnetic switching statistics of an individual, non-single-domain Fe$_3$O$_4$ nanoparticle using a micrometer-scale superconducting quantum interference device. Surprisingly, a strong narrowing of the waiting-time distributions before reaching the final state is observed as compared to the exponential distribution expected for a single barrier. The magnetization reversal across the nanostructure is thus shown to result from multiple serial barriers in the minimum energy pathway.

Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways.

With the increasing popularity of machine learning (ML) applications, the demand for explainable artificial intelligence techniques to explain ML models developed for computational chemistry has also emerged. In this study, we present the development of the Boltzmann-weighted cumulative integrated gradients (BCIG) approach for effective explanation of mechanistic insights into ML models trained on high-level quantum mechanical and molecular mechanical (QM/MM) minimum energy pathways. Using the acylation reactions of the Toho-1 β-lactamase and two antibiotics (ampicillin and cefalexin) as the model systems, we show that the BCIG approach could quantitatively attribute the energetic contribution in one system and the relative reactivity of individual steps across different systems to specific chemical processes such as the bond making/breaking and proton transfers. The proposed BCIG contribution attribution method quantifies chemistry-interpretable insights in terms of contributions from each elementary chemical process, which is in agreement with the validating QM/MM calculations and our intuitive mechanistic understandings of the model reactions.

Ferroelectric HfO2 and the importance of strain

Ferroelectric oxides based on ${\mathrm{HfO}}_{2}$ show tremendous promise for the next generation of memory and logic devices. The ferroelectric polymorph is one of several that can be derived from the high symmetry cubic fluorite structure of ${\mathrm{HfO}}_{2}$. A single grain of ${\mathrm{HfO}}_{2}$ may consist of a coherent mixture of multiple orientational and translational variants of different polymorphs. Here, we use symmetry-adapted strain-order parameters to elucidate the relationship between the different ${\mathrm{HfO}}_{2}$ polymorphs and their symmetrically equivalent variants. We use first-principles electronic structure methods to identify minimum energy pathways and map them in subspaces of the symmetry-adapted strain order parameters. We next investigate the atomic structure of domain boundaries that separate coexisting variants of ferroelectric ${\mathrm{HfO}}_{2}$. We rely on Gibbsian excess quantities and a precise specification of mechanical boundary conditions to describe the thermodynamic properties of domain boundaries. Our first-principles calculations show that the O and Hf shuffle arrangement within a domain boundary is closely related to the intermediate shuffle patterns of the homogeneous pathways between ferroelectric variants. Furthermore, the preferred structure within a boundary is very sensitive to local strain constraints imposed by the adjacent ferroelectric variants, leading to highly anisotropic domain boundary energies.

High-Performance of Electrocatalytic CO2 Reduction on Defective Graphene-Supported Cu4S2 Cluster

Electrochemical CO2 reduction reaction (CO2RR) to high-value chemicals is one of the most splendid approaches to mitigating environmental threats and energy shortage. In this study, the catalytic performance of CO2RR on defective graphene-supported Cu4S2 clusters as well as isolated Cu4Xn (X = O, S, Se; n = 2, 4) was systematically investigated based on density functional theory (DFT) computations. Calculation results revealed that the most thermodynamically feasible product is CH3OH among the C1 products on Cu4X2 clusters, in which the Cu4S2 cluster has the best activity concerning CH3OH synthesis with a limiting potential of −0.48 V. When the Cu4S2 cluster was further supported on defective graphene, the strong interaction between cluster and substrate could greatly improve the performance via tuning the electronic structure and improving the stability of the Cu4S2 cluster. The calculated free energy diagram indicated that it is also more energetically preferable for CH3OH production with a low limiting potential of −0.35 V. Besides, the defective graphene support has a significant ability to suppress the competing reactions, such as the hydrogen evolution reaction (HER) and CO and HCOOH production. Geometric structures, limiting potentials, and reduction pathways were also discussed to gain insight into the reaction mechanism and to find the minimum-energy pathway for C1 products. We hope this work will provide theoretical reference for designing and developing advanced supported Cu-based electrocatalysts for CO2 reduction.