Unsupervised learning of representative local atomic arrangements in molecular dynamics data.

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. We combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

X-ray absorption spectroscopy insights on the structure anisotropy and charge transfer in Chevrel Phase chalcogenides.

The electronic structure and local coordination of binary (Mo6T8) and ternary Chevrel Phases (MxMo6T8) are investigated for a range of metal intercalant and chalcogen compositions. We evaluate differences in the Mo L3-edge and K-edge X-ray absorption near edge structure across the suite of chalcogenides MxMo6T8 (M = Cu, Ni, x = 1-2, T = S, Se, Te), quantifying the effect of compositional and structural modification on electronic structure. Furthermore, we highlight the expansion, contraction, and anisotropy of Mo6 clusters within these Chevrel Phase frameworks through extended X-ray absorption fine structure analysis. Our results show that metal-to-cluster charge transfer upon intercalation is dominated by the chalcogen acceptors, evidenced by significant changes in their respective X-ray absorption spectra in comparison to relatively unaffected Mo cations. These results explain the effects of metal intercalation on the electronic and local structure of Chevrel Phases across various chalcogen compositions, and aid in rationalizing electron distribution within the structure.

Ca-dimers, solvent layering, and dominant electrochemically active species in Ca(BH4)2 in THF.

Divalent ions (Mg, Ca, and Zn) are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry, but present challenges for stable cycling due to undesirable interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2∣THF using molecular dynamics coupled with a continuum model of bulk and interfacial speciation. Free-energy analysis and unsupervised learning indicate a majority population of neutral Ca dimers and monomers with diverse molecular conformations and an order of magnitude lower concentration of the primary electroactive charged species - the monocation, CaBH[Formula: see text] - produced via disproportionation of neutral complexes. Dense layering of THF molecules within ~1 nm of the electrode surface strongly modulates local electrolyte species populations. A dramatic increase in monocation population in this interfacial zone is induced at negative bias. We see no evidence for electrochemical activity of fully-solvated Ca2+. The consequences for performance are discussed in light of this molecular-scale insight.

Spontaneous and scanning-assisted desorption-adsorption dynamics in porous supramolecular networks at the solution-solid interface.

Self-assembled molecular networks (SAMNs) are formed by the spontaneous assembly of molecules on surfaces. On conductive atomically flat surfaces, and also at the liquid-solid interface, scanning tunneling microscopy (STM) can follow their growth dynamics. Desorption and adsorption dynamics are difficult to probe through the liquid-solid interface. Porous molecular networks are of particular interest because they may act as platforms for sensing and host-guest chemistry. Very little is known though about their stability, particularly in a liquid environment. To this end, we have investigated the desorption/adsorption dynamics of supramolecular porous monolayers of alkoxylated dehydrobenzo[12]annulene (DBA) derivatives at the interface between highly oriented pyrolytic graphite, the substrate, and 1-phenyloctane, the liquid. To trace the dynamics, structurally analogous chiral DBA derivatives were used as marker molecules, which co-assemble with the achiral ones forming the supramolecular network. This approach reveals the time scales of the adsorption/desorption dynamics, the significance of temperature, and the important role of the STM tip in inducing dynamics.

Gold-like activity copper-like selectivity of heteroatomic transition metal carbides for electrocatalytic carbon dioxide reduction reaction.

An overarching challenge of the electrochemical carbon dioxide reduction reaction (eCO2RR) is finding an earth-abundant, highly active catalyst that selectively produces hydrocarbons at relatively low overpotentials. Here, we report the eCO2RR performance of two-dimensional transition metal carbide class of materials. Our results indicate a maximum methane (CH4) current density of -421.63 mA/cm2 and a CH4 faradic efficiency of 82.7% ± 2% for di-tungsten carbide (W2C) nanoflakes in a hybrid electrolyte of 3 M potassium hydroxide and 2 M choline-chloride. Powered by a triple junction photovoltaic cell, we demonstrate a flow electrolyzer that uses humidified CO2 to produce CH4 in a 700-h process under one sun illumination with a CO2RR energy efficiency of about 62.3% and a solar-to-fuel efficiency of 20.7%. Density functional theory calculations reveal that dissociation of water, chemisorption of CO2 and cleavage of the C-O bond-the most energy consuming elementary steps in other catalysts such as copper-become nearly spontaneous at the W2C surface. This results in instantaneous formation of adsorbed CO-an important reaction intermediate-and an unlimited source of protons near the tungsten surface sites that are the main reasons for the observed superior activity, selectivity, and small potential.

Halogenated building blocks for 2D crystal engineering on solid surfaces: lessons from hydrogen bonding.

Halogen bonding has emerged as a promising tool in two-dimensional (2D) crystal engineering. Since halogen bonds are similar to hydrogen bonds in a number of aspects, the existing knowledge of hydrogen bonded systems can be applied to halogenated systems. Here we evaluate the applicability of a retrosynthetic approach based on topological similarity between hydrogen and halogen bonds to obtain predictable halogen bonded networks. The self-assembly of 1,3-dibromo-5-alkoxybenzene derivatives was studied in analogy with well-explored alkoxy isophthalic acids using a combination of experimental and theoretical tools. Scanning tunneling microscopy (STM) characterization of the networks formed at the liquid-graphite interface revealed that while the retrosynthetic approach works at the level of small clusters of molecules within the 2D network, the overall structure of the network deviates from the anticipated structure. The monolayers consist of fractured rows of halogen-bonded modules instead of the expected continuous lamellar structure. Each module consists of a discrete number of halogen-bonded molecules. The interactions responsible for the stabilization of halogen bonded dimers are delineated through detailed density functional theory (DFT) calculations coupled with natural bonding orbitals (NBO) and perturbation analysis. A modified force field that includes an extra charged site to imitate the σ hole on the halogen atom was developed and applied to extract total potential energies of the anticipated and observed networks. Plausible reasons for the deviation from the anticipated structure are discussed. Finally, a modified molecular design that allows successful application of the hydrogen bond-halogen bond analogy was tested experimentally.

Computational insight into the origin of unexpected contrast in chiral markers as revealed by STM.

Internal substituents can serve the double purpose of generating stereogenic centers and (potentially) being identifiable with Scanning Tunneling Microscopy (STM) in 2D self-assembled molecular layers. We investigate computationally the origin of stark contrast variations in STM images of chirally substituted self-assembled organic films. STM images of alkyl derivatives with secondary -CH3 and -OH groups have been simulated. Density functional theory calculations reveal bias-dependent contrast reversals in the substituent regions: a lack of local density of states in the relevant energy regime results in 'dark spots' in the simulated STM images, which turn bright upon increasing the bias voltage.