Molecular Lattice Research Articles

Equivariant Neural Networks Utilizing Molecular Clusters for Accurate Molecular Crystal Lattice Energy Predictions.

Equivariant neural networks have emerged as prominent models in advancing the construction of interatomic potentials due to their remarkable data efficiency and generalization capabilities for out-of-distribution data. Here, we expand the utility of these networks to the prediction of crystal structures consisting of organic molecules. Traditional methods for computing crystal structure properties, such as plane-wave quantum chemical methods based on density functional theory (DFT), are prohibitively resource-intensive, often necessitating compromises in accuracy and the choice of exchange-correlation functional. We present an approach that leverages the efficiency, and transferability of equivariant neural networks, specifically Allegro, to predict molecular crystal structure energies at a reduced computational cost. Our neural network is trained on molecular clusters using a highly accurate Gaussian-type orbital (GTO)-based method as the target level of theory, eliminating the need for costly periodic DFT calculations, while providing access to all families of exchange-corelation functionals and post-Hartree-Fock methods. The trained model exhibits remarkable accuracy in predicting lattice energies, aligning closely with those computed by plane-wave based DFT methods, thus representing significant cost reductions. Furthermore, the Allegro network was seamlessly integrated with the USPEX framework, accelerating the discovery of low-energy crystal structures during crystal structure prediction.

Molecular O2 Dimers and Lattice Instability in a Perovskite Electrocatalyst.

Structural degradation of oxide electrodes during the electrocatalytic oxygen evolution reaction (OER) is a major challenge in water electrolysis. Although the OER is known to induce changes in the surface layer, little is known about its effect on the bulk of the electrocatalyst and its overall phase stability. Here, we show that under OER conditions, a highly active SrCoO3-x electrocatalyst develops bulk lattice instability, which results in the formation of molecular O2 dimers inside the bulk and nanoscale amorphization induced via chemo-mechanical coupling. Using high-resolution resonant inelastic X-ray scattering and first-principles calculations, we unveil the potential-dependent evolution of lattice oxygen inside the perovskite and demonstrate that O2 dimers are stable in a densely packed crystal lattice, thus challenging the assumption that O2 dimers require sufficient interatomic spacing. We also show that the energy cost of local atomic rearrangements in SrCoO3-x becomes very low under the OER conditions, leading to an unusual amorphization under intercalation-induced stress. As a result, we propose that the amorphization energy can be calculated from the first principles and can be used to assess the stability of electrocatalysts. Our study demonstrates that extreme oxidation of electrocatalysts under OER can intrinsically destabilize the lattice and result in bulk anion redox and disorder, suggesting why some oxide materials are unstable and develop a thick amorphous layer under water electrolysis conditions.

Searching for new fundamental interactions via isotopic shifts in molecular lattice clocks

Precision measurements with ultracold atoms and molecules are primed to probe beyond-the-standard model physics. Isotopologues of homonuclear molecules are a natural testbed for new Yukawa-type mass-dependent forces at nanometer scales, complementing existing mesoscopic-body and neutron scattering experiments. Here, we propose using isotopic shift measurements in molecular lattice clocks to constrain these new interactions from new massive scalar particles in the keV/c2 range: The new interaction would impart an extra isotopic shift to molecular levels on top of one predicted by the standard model. For the strontium dimer, a Hz-level agreement between experiment and theory could constrain the coupling of the new particles to hadrons by up to an order of magnitude over the most stringent existing experiments. Published by the American Physical Society 2024

3D Nanocrystallography and the Imperfect Molecular Lattice.

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

Unconventional Band Structure via Combined Molecular Orbital and Lattice Symmetries in a Surface-Confined Metallated Graphdiyne Sheet.

Graphyne (GY) and graphdiyne (GDY)-based monolayers represent the next generation 2D carbon-rich materials with tunable structures and properties surpassing those of graphene. However, the detection of band formation in atomically thin GY/GDY analogues has been challenging, as both long-range order and atomic precision have to be fulfilled in the system. The presentwork reports direct evidence of band formation in on-surface synthesized metallated Ag-GDY sheets with mesoscopic (≈1µm) regularity. Employing scanning tunneling and angle-resolved photoemission spectroscopies, energy-dependent transitions of real-space electronic states above the Fermi level and formation of the valence band are respectively observed. Furthermore, density functional theory (DFT) calculations corroborate the observations and reveal that doubly degenerate frontier molecular orbitals on a honeycomb lattice give rise to flat, Dirac and Kagome bands close to the Fermi level. DFT modeling also indicates an intrinsic band gap for the pristine sheet material, which is retained for a bilayer with h-BN, whereas adsorption-induced in-gap electronic states evolve at the synthesis platform with Ag-GDY decorating the (111) facet of silver. These results illustrate the tremendous potential for engineering novel band structures via molecular orbital and lattice symmetries in atomically precise 2D carbon materials.

Molecular heat transport across a time-periodic temperature gradient.

The time-periodic modulation of a temperature gradient can alter the heat transport properties of a physical system. Oscillating thermal gradients give rise to behaviors such as modified thermal conductivity and controllable time-delayed energy storage that are not present in a system with static temperatures. Here, we examine how the heat transport properties of a molecular lattice model are affected by an oscillating temperature gradient. We use analytical analysis and molecular dynamics simulations to investigate the vibrational heat flow in a molecular lattice system consisting of a chain of particles connected to two heat baths at different temperatures, where the temperature difference between baths is oscillating in time. We derive expressions for heat currents in this system using a stochastic energetics framework and a nonequilibrium Green's function approach that is modified to treat the nonstationary average energy fluxes. We find that emergent energy storage, energy release, and thermal conductance mechanisms induced by the temperature oscillations can be controlled by varying the frequency, waveform, and amplitude of the oscillating gradient. The developed theoretical approach provides a general framework to describe how vibrational heat transmission through a molecular lattice is affected by temperature gradient oscillations.

Atomic wetting of oil droplets into hexagons and stripes

HypothesisPrevious studies showed that liquid droplets can be spherical caps or polygonal shapes on patterned surfaces. We hypothesize that these phenomena can be narrowed down to nanoscale and affecting liquid molecular wetting. We anticipate observing preferential wetting on the underlying substrate with atomic crystalline lattice. ExperimentsThis study explores the wetting behavior of oil nanodroplets deposited on highly ordered pyrolytic graphite (HOPG) with atomic force microscope (AFM). Oil droplets were scanned with hydrophobic and hydrophilic AFM tips in water in peak force mode AFM, carefully controlling the scanning force. Simple modeling was carried out using Surface Evolver to simulate how oil droplets wet on HOPG with molecular lattice. FindingsThe results showed two distinct wetting behaviors: the hexagonal nanodroplets and stripe nanometric films. In both cases, the droplets appear to wet preferentially along preferred orientations which reflect the atomic periodicity of the underlying substrate. This preferential wetting occurs because the atomic roughness is significant at the length scale of the nanodroplets, while the eventual outcome of the wetting (i.e. whether the droplet settles to a finite contact angle, or wets completely into a nanometric film) is dependent on the spreading parameter of the droplet-substrate system, independent of scanning direction.

Pushing thermal conductivity to its lower limit in crystals with simple structures

Materials with low thermal conductivity usually have complex crystal structures. Herein we experimentally find that a simple crystal structure material AgTlI2 (I4/mcm) owns an extremely low thermal conductivity of 0.25 W/mK at room temperature. To understand this anomaly, we perform in-depth theoretical studies based on ab initio molecular dynamics simulations and anharmonic lattice dynamics. We find that the unique atomic arrangement and weak chemical bonding provide a permissive environment for strong oscillations of Ag atoms, leading to a considerable rattling behaviour and giant lattice anharmonicity. This feature is also verified by the experimental probability density function refinement of single-crystal diffraction. The particularly strong anharmonicity breaks down the conventional phonon gas model, giving rise to non-negligible wavelike phonon behaviours in AgTlI2 at 300 K. Intriguingly, unlike many strongly anharmonic materials where a small propagative thermal conductivity is often accompanied by a large diffusive thermal conductivity, we find an unusual coexistence of ultralow propagative and diffusive thermal conductivities in AgTlI2 based on the thermal transport unified theory. This study underscores the potential of simple crystal structures in achieving low thermal conductivity and encourages further experimental research to enrich the family of materials with ultralow thermal conductivity.

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling.

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

Meltable Aluminum Molecular Rings with Fluorescence and Nonlinear Optical Properties.

Crystal-liquid-glass, which combines the tunable properties of crystalline compounds with the processability of glasses, has emerged as a new class of materials for fabricating bulk-shapable devices in real applications. Inspired by the characteristics of deep eutectic solvent (DES) mixtures involving significant depressions in melting points compared to their neat constituent components, in this study, we designed and synthesized the first examples of meltable aluminum oxo clusters (AlOCs) via lattice doping with DESs at the molecular level. The abundant and strong hydrogen bonding between the aluminum molecular ring, DES components, and lattice solvents is postulated to be the root that affords melting point depressions and, thus, "melting" clusters. We prepared a transparent bubble-free glass film under autogenous pressure using a hot-press method. These cluster-based films exhibited luminescent and nonlinear optical properties similar to those of pristine crystalline compounds. Our study belongs to the interdisciplinary disciplines of chemistry and physics. It not only breaks the limitations of crystalline glass on metal and ligand types but also acts as a general guide for extending the range of meltable crystalline materials.

Meltable Aluminum Molecular Rings with Fluorescence and Nonlinear Optical Properties

AbstractCrystal–liquid–glass, which combines the tunable properties of crystalline compounds with the processability of glasses, has emerged as a new class of materials for fabricating bulk‐shapable devices in real applications. Inspired by the characteristics of deep eutectic solvent (DES) mixtures involving significant depressions in melting points compared to their neat constituent components, in this study, we designed and synthesized the first examples of meltable aluminum oxo clusters (AlOCs) via lattice doping with DESs at the molecular level. The abundant and strong hydrogen bonding between the aluminum molecular ring, DES components, and lattice solvents is postulated to be the root that affords melting point depressions and, thus, “melting” clusters. We prepared a transparent bubble‐free glass film under autogenous pressure using a hot‐press method. These cluster‐based films exhibited luminescent and nonlinear optical properties similar to those of pristine crystalline compounds. Our study belongs to the interdisciplinary disciplines of chemistry and physics. It not only breaks the limitations of crystalline glass on metal and ligand types but also acts as a general guide for extending the range of meltable crystalline materials.

Accurate Determination of Blackbody Radiation Shifts in a Strontium Molecular Lattice Clock.

Molecular lattice clocks enable the search for new physics, such as fifth forces or temporal variations of fundamental constants, in a manner complementary to atomic clocks. Blackbody radiation (BBR) is a major contributor to the systematic error budget of conventional atomic clocks and is notoriously difficult to characterize and control. Here, we combine infrared Stark-shift spectroscopy in a molecular lattice clock and modern quantum chemistry methods to characterize the polarizabilities of the Sr_{2} molecule from dc to infrared. Using this description, we determine the static and dynamic blackbody radiation shifts for all possible vibrational clock transitions to the 10^{-16} level. This constitutes an important step toward millihertz-level molecular spectroscopy in Sr_{2} and provides a framework for evaluating BBR shifts in other homonuclear molecules.

Tailoring Ag Electron Donating Ability for Organohalide Reduction: A Bilayer Electrode Design.

Electrochemical reduction of organohalides provides a green approach in the reduction of environmental pollutants, the synthesis of new organic molecules, and many other applications. The presence of a catalytic electrode can make the process more energetically efficient. Ag is known to be a very good electrode for the reduction of a wide range of organohalides. Herein, we examine the elementary adsorption and reaction steps that occur on Ag and the changes that result from changes in the Ag-coated metal, strain in Ag, solvent, and substrate geometry. The results are used to develop an electrode design strategy that can possibly be used to further increase the catalytic activity of pure Ag electrodes. We have shown how epitaxially depositing one to three layers of Ag on catalytically inert or less active support metal can increase the surface electron donating ability, thus increasing the adsorption of organic halide and the catalytic activity. Many factors, such as molecular geometry, lattice mismatches, work function, and solvents, contribute to the adsorption of organic halide molecules over the bilayer electrode surface. To isolate and rank these factors, we examined three model organic halides, namely, halothane, bromobenzene (BrBz), and benzyl bromide (BzBr) adsorption on Ag/metal (metal = Au, Bi, Pt, and Ti) bilayer electrodes in both vacuum and acetonitrile (ACN) solvent. The different metal supports offer a range of lattice mismatches and work function differences with Ag. Our calculations show that the surface of Ag becomes more electron donating and accessible to adsorption when it forms a bilayer with Ti as it has a lower work function and almost zero lattice mismatch with Ag. We believe this study will help to increase the electron donating ability of the Ag surface by choosing the right metal support, which in turn can improve the catalytic activity of the working electrode.

Collective States in Molecular Monolayers on 2D Materials.

Collective excited states form in organic two-dimensional layers through Coulomb coupling of the molecular transition dipole moments. They manifest as characteristic strong and narrow peaks in the excitation and emission spectra that are shifted to lower energies compared with the monomer transition. We study experimentally and theoretically how robust the collective states are against homogeneous and inhomogeneous broadening, as well as spatial disorder that occurs in real molecular monolayers. Using a microscopic model for a two-dimensional dipole lattice in real space, we calculate the properties of collective states and their extinction spectra. We find that the collective states persist even for 1-10% random variation in the molecular position and in the transition frequency, with a peak position and integrated intensity similar to those for the perfectly ordered system. We measured the optical response of a monolayer of the perylene derivative MePTCDI on two-dimensional materials. On the wide-band-gap insulator hexagonal boron nitride, it shows strong emission from the collective state with a line width that is dominated by the inhomogeneous broadening of the molecular state. When the semimetal graphene is used as a substrate, however, the luminescence is completely quenched. By combining optical absorption, luminescence, and multiwavelength Raman scattering, we verify that the MePTCDI molecules form very similar collective monolayer states on hexagonal boron nitride and graphene substrates, but on graphene the line width is dominated by nonradiative excitation transfer from the molecules to the substrate. Our study highlights the transition from the localized molecular state of the monomer to a delocalized collective state in the two-dimensional molecular lattice that is entirely based on Coulomb coupling between optically active excitations of the electrons and molecular vibrations. The excellent properties of organic monolayers make them promising candidates for components of soft-matter optoelectronic devices.

Enlargement of Structure-H Clathrate Hydrates by New Large Molecular Guest Substances and Lattice Size Limitation

The size of structure-H clathrate hydrates (sH hydrates) depends on the size of large molecule guest substances (LMGSs) that are en-captured in icosahedral (51268, E) cages. Especially, the c-axis in an sH hydrate structure is sensitive toward the longest molecular length of the LMGSs. In this study, we report four new LMGSs for structure-H hydrates containing CH4, namely, iodocyclopentane (ICP), chlorocycloheptane (ClCHP), bromocycloheptane (BrCHP), and trans-1,4-dichlorocyclohexane (t14DClCH). The longest molecular length of t14DClCH is 0.975 nm, considering its van der Waals radius. Moreover, t14DClCH is assumed to be the longest possible LMGS for sH hydrates containing CH4 because of the relationship between its lattice parameter and its longest molecular length. The phase equilibrium pressure–temperature conditions in the four CH4–LMGS–water systems were also measured by an isochoric method. The temperature shifts of the four LMGS systems from the pure CH4–water system increased in the following order: ICP ∼ BrCHP (3.7 K) < ClCHP (4.7 K) < t14DClCH (5.1 K).

Quantum Criticality and Universal Behavior in Molecular Dipolar Lattices of Endofullerenes

Fullerene cages allow the confinement of single molecules and the construction of molecular assemblies whose properties strongly differ from those of free species. In this work, we employ the density-matrix renormalization group method to show that chains of fullerenes filled with polar molecules (LiF, HF, and H2O) can form dipole-ordered quantum phases. In symmetry broken environments, these ordered phases are ferroelectric, a property that makes them promising candidates for quantum devices. We demonstrate that for a given guest molecule, the occurrence of these quantum phases can be enforced or influenced either by changing the effective electric dipole moment or by isotopic substitution. In the ordered phase, all systems under consideration are characterized by universal behavior that depends only on the ratio of the effective electric dipole and of the rotational constant. A phase diagram is derived, and further molecules are proposed as candidates for dipole-ordered endofullerene chains.

Control of the vortex lattice formation in coupled atom-molecular Bose–Einstein condensate in a double well potential: role of atom-molecule coupling, trap rotation frequency and detuning parameter

We study the vortex formation in coupled atomic and molecular condensates in a rotating double well trap by numerically solving the coupled Gross–Pitaevskii like equations. Starting with the atomic condensate in the double well potential we considered two-photon Raman photo-association for coherent conversion of atoms to molecules. It is shown that the competition between atom-molecule coupling strength and repulsive atom-molecule interaction controls the spacings between atomic and molecular vortices and the rotation frequency of the trap is the key player for controlling the number of visible atomic and molecular vortices. Whereas the Raman detuning controls the spacing between atomic and molecular vortices as well as the number of atomic and molecular vortices in the trap. We have shown by considering the molecular lattices the distance between two molecular vortices can be controlled by varying the Raman detuning. In addition we have found that the Feynman rule relating the total number of vortices and average angular momentum both for atoms and molecules can be satisfied by considering the atomic and molecular vortices those are hidden in density distribution and seen as singularities in phase distribution of the coupled system except for the lattice structure where molecular vortices are overlapped with each other. It is found that although the number of visible/core vortices in atomic and molecular vortex lattices depends significantly on the system parameters the number of atomic and molecular hidden vortices remains constant in most of the cases.

Pressure-controlled magnetism in 2D molecular layers

Long-range magnetic ordering of two-dimensional crystals can be sensitive to interlayer coupling, enabling the effective control of interlayer magnetism towards voltage switching, spin filtering and transistor applications. With the discovery of two-dimensional atomically thin magnets, a good platform provides us to manipulate interlayer magnetism for the control of magnetic orders. However, a less-known family of two-dimensional magnets possesses a bottom-up assembled molecular lattice and metal-to-ligand intermolecular contacts, which lead to a combination of large magnetic anisotropy and spin-delocalization. Here, we report the pressure-controlled interlayer magnetic coupling of molecular layered compounds via chromium-pyrazine coordination. Room-temperature long-range magnetic ordering exhibits pressure tuning with a coercivity coefficient up to 4 kOe/GPa, while pressure-controlled interlayer magnetism also presents a strong dependence on alkali metal stoichiometry and composition. Two-dimensional molecular interlayers provide a pathway towards pressure-controlled peculiar magnetism through charge redistribution and structural transformation.

Anti-Stokes/Stokes temperature calibration and its application in laser-heating diamond anvil cells

Anti-Stokes/Stokes Raman peak intensity ratio was used to infer sample temperatures, but the influence factors of system correction factors were not clear. Non-contact in-situ anti-Stokes/Stokes temperature calibration was carried out for up to 1500 K based on six different samples under two excitation light sources (±50 K within 1000 K, ±100 K above 1000 K), and the system correction factor γ was systematically investigated. The results show that the correction factor γ of anti-Stokes/Stokes thermometry is affected by the wavelength of the excitation light source, Raman mode peak position, temperature measurement region and other factors. The anti-Stokes/Stokes thermometry was applied to the laser-heating diamond anvil cell (LHDAC) experiment to investigate the anharmonic effect of hBN under high temperature and high pressure. It is concluded that the strong anharmonic effect caused by phonon scattering at low pressure gradually changes into the predominance of localized molecular lattice thermal expansion at high pressure.

EFFECT OF DIFFERENT CHEMICALS ON THE CARBONIZATION BEHAVIORS AND POLLUTION REMOVAL PERFORMANCE OF BIOCHAR ADSORBENTS DERIVED FROM TEXTILE WASTE

One of the smart methods of controlling the increasing demand for raw materials and environmental pollution is the recycling of waste. In this study, optimum conditions were determined for the conversion of wastes that will not be reused in the textile industry into functional activated carbon. For this, raw and Fe, H2SO4, H3PO4 impregnated textile wastes were carbonized at different temperatures for varying times. The molecular structure and crystal lattice of the prepared activated carbons were investigated by FT-IR and XRD analyzes, respectively. SEM and BET analyzes were used to examine the morphology and surface properties of the samples. The existence of C=C, C=O, and C–O–C functional groups was recognized by the vibrations at around 1300-1700 cm-1. A well-crystalline and porous structure was formed as a result of the carbonization of the Fe and H3PO4 pretreated samples, while the process was conducted at a lower temperature due to the catalytic effect. 25–85 mg/g methyl orange (MO) and industrial textile water (ITW) removal capacity were recorded for all samples. Efficient biochars were obtained by carbonization of waste materials while protecting the environment. Such a specific approach could be developed for each waste material for environmental and economic production