Molecule-molecule Interactions Research Articles

Understanding solid nitrogen through molecular dynamics simulations with a machine-learning potential

We construct a fast, transferable, general purpose, machine-learning interatomic potential suitable for large-scale simulations of N2. The potential is trained only on high quality quantum chemical molecule-molecule interactions; no condensed phase information is used. Although there are no explicit or implicit many-molecule interaction terms, the potential reproduces the experimental phase diagram including the melt curve and the molecular solid phases of nitrogen up to 10GPa. This demonstrates that many-molecule interactions are unnecessary to explain the condensed phases of N2. With increased pressure, transitions are observed from cubic (α), which optimizes quadrupole-quadrupole interactions, through tetragonal (γ), which allows more efficient packing, to monoclinic (λ), which packs still more efficiently. On heating, we obtain the hcp three-dimensional (3D) rotor phase (β) and, at pressure, the cubic δ phase which contains both 3D and 2D rotors, tetragonal δ* phase with 2D rotors, and the rhombohedral ε. Molecular dynamics demonstrates where these phases are indeed rotors, rather than frustrated order. The model supports the metastability of the complex ι phase, but not the reported existence of the wide range of bond lengths. The thermodynamic transitions involve both shifts of molecular centers and rotations of molecules: the onset of rotation is rapid, whereas motion of molecular centers is inhibited and we suggest that this is the cause of the experimentally observed sluggishness of transitions. Routine density functional theory calculations give a similar picture to the potential. Published by the American Physical Society 2024

Quantifying Hydrogen-Bonding Interactions in the Self-Assembly of Photoresponsive Azobenzene Amphiphiles at the Air-Water Interface.

Amphiphilic azobenzene molecules offer ample scope to design functional supramolecular systems in an aqueous medium that can be controlled by light. Despite their widespread applications in photopharmacology and optoelectronics, the self-assembly pathways and energy landscapes of these systems are not well understood. Here, we report combined molecular dynamics (MD) simulation and surface manometry studies on a specially designed alkylated, meta-substituted azobenzene derivative to quantify the hydrogen-bonding interactions in the self-assembled monolayers of its photoisomers. The z-density profile, radial distribution function, order parameters, and hydrogen bond analyzed using MD simulations corroborated the experimental observations of changes in surface pressure, dipole moment, and thickness of the monolayers. Even a small change in the number of hydrogen bonds in the molecule-molecule and molecule-water interactions causes significant changes in the monolayer properties. These results are fundamentally important for engineering photoresponsive molecules with tailored properties for applications in targeted drug delivery and other industrial applications.

Tailoring Interface Energies via Phosphonic Acids to Grow and Stabilize Cubic FAPbI3 Deposited by Thermal Evaporation.

Coevaporation of formamidinium lead iodide (FAPbI3) is a promising route for the fabrication of highly efficient and scalable optoelectronic devices, such as perovskite solar cells. However, it poses experimental challenges in achieving stoichiometric FAPbI3 films with a cubic structure (α-FAPbI3). In this work, we show that undesired hexagonal phases of both PbI2 and FAPbI3 form during thermal evaporation, including the well-known 2H-FAPbI3, which are detrimental for optoelectronic performance. We demonstrate the growth of α-FAPbI3 at room temperature via thermal evaporation by depositing phosphonic acids (PAc) on substrates and subsequently coevaporating PbI2 and formamidinium iodide. We use density-functional theory to develop a theoretical model to understand the relative growth energetics of the α and 2H phases of FAPbI3 for different molecular interactions. Experiments and theory show that the presence of PAc molecules stabilizes the formation of α-FAPbI3 in thin films when excess molecules are available to migrate during growth. This migration of molecules facilitates the continued presence of adsorbed organic precursors at the free surface throughout the evaporation, which lowers the growth energy of the α-FAPbI3 phase. Our theoretical analyses of PAc molecule-molecule interactions show that ligands can form hydrogen bonding to reduce the migration rate of the molecules through the deposited film, limiting the effects on the crystal structure stabilization. Our results also show that the phase stabilization with molecules that migrate is long-lasting and resistant to moist air. These findings enable reliable formation and processing of α-FAPbI3 films via vapor deposition.

Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available.

Assessing plasmon-induced reactions by a combined quantum chemical-quantum/classical hybrid approach.

Plasmon-driven reactions on metal nanoparticles feature rich and complex mechanistic contributions, involving a manifold of electronic states, near-field enhancement, and heat, among others. Although localized surface plasmon resonances are believed to initiate these reactions, the complex reactivity demands deeper exploration. This computational study investigates factors influencing chemical processes on plasmonic nanoparticles, exemplified by protonation of 4-mercaptopyridine (4-MPY) on silver nanoparticles. We examine the impact of molecular binding modes and molecule-molecule interactions on the nanoparticle's surface, near-field electromagnetic effects, and charge-transfer phenomena. Two proton sources were considered at ambient conditions, molecular hydrogen and water. Our findings reveal that the substrate's binding mode significantly affects not only the energy barriers governing the thermodynamics and kinetics of the reaction but also determine the directionality of light-driven charge-transfer at the 4-MPY-Ag interface, pivotal in the chemical contribution involved in the reaction mechanism. In addition, significant field enhancement surrounding the adsorbed molecule is observed (eletromagnetic contribution) which was found insufficient to modify the ground state thermodynamics. Instead, it initiates and amplifies light-driven charge-transfer and thus modulates the excited states' reactivity in the plasmonic-molecular hybrid system. This research elucidates protonation mechanisms on silver surfaces, highlighting the role of molecular-surface and molecule-molecule-surface orientation in plasmon-catalysis.

Tensor renormalization group study of orientational ordering in simple models of adsorption monolayers.

A simple lattice model of the orientational ordering in organic adsorption layers that considers the directionality of intermolecular interactions is proposed. The symmetry and the number of rotational states of the adsorbed molecule are the main parameters of the model. The model takes into account both the isotropic and directional contributions to the molecule-molecule interaction potential. Using several special cases of this model, we have shown that the tensor renormalization group (TRG) approach can be successfully used for the analysis of orientational ordering in organic adsorption layers with directed intermolecular interactions. Adsorption isotherms, potential energy, and entropy have been calculated for the model adsorption layers differing in the molecule symmetry and the number of rotational states. The calculated thermodynamic characteristics show that entropy effects play a significant role in the self-assembly of dense phases of the molecular layers. All the results obtained with the TRG have been verified by the standard Monte Carlo method. The proposed model reproduces the main features of the phase behavior of the real adsorption layers of benzoic, terephthalic, and trimesic acids on a homogeneous surface of metal single crystals and graphite.

Order-Disorder, Symmetry Breaking, and Crystallographic Phase Transition in a Series of Bis(trans-thiocyanate)iron(II) Spin Crossover Complexes Based on Tetradentate Ligands Containing 1,2,3-Triazoles.

We report herein a series of neutral trans-thiocyanate mononuclear spin crossover (SCO) complexes, [FeIIL(NCS)2] (1-4), based on tetradentate ligands L obtained by reaction of N-substituted 1,2,3-triazolecarbaldehyde with 1,3-propanediamine or 2,2-dimethyl-1,3-diaminopropane [L = N1,N3-bis((1,5-dimethyl-1H-1,2,3-triazol-4-yl)methylene)propane-1,3-diamine/-2,2-dimethylpropane-1,3-diamine, 1/2 and N1,N3-bis((1-ethyl/1-propyl-1H-1,2,3-triazol-4-yl)methylene)-2,2-dimethylpropane-1,3-diamine, 3/4]. The thermal-induced SCO behavior is characterized by abrupt transitions with an average critical temperature (ΔT1/2)/hysteresis loop width (ΔThyst) in the range 190-252/5-14 K, while the photo-generated metastable high-spin (HS) phases are characterized by TLIESST temperatures in the range 44-59 K. Single crystal analysis shows that except 1, all compounds experience reversible symmetry breaking coupled with the thermal SCO. Furthermore, 4 experiences an additional phase transition at ca. 290 K responsible for the coexistence of two HS phases quenched at 10 K through LIESST and TIESST effects. The molecules form hexagonally packed arrays sustained by numerous weak CH···S and C···C/S···C/N···C bonds involving polar coordination cores, while non-polar pendant aliphatic substituents are segregated inside, occupying hexagonal channels. Energy framework analysis of complexes with one step SCO transition (1, 2, and 4) shows a correlation between the cooperativity and the amplitude of changes in the molecule-molecule interactions in the lattice at the SCO transition.

Role of Molecular, Crystal, and Surface Chemistry in Directing the Crystallization of Entacapone Polymorphs on the Au(111) Template Surface.

The pharmaceutical compound entacapone ((E)-2-cyano-3-(3,4-dihydroxy-5-nitrophenyl)-N,N-diethylprop-2-enamide) is important in the treatment of Parkinson's disease, exhibiting interesting polymorphic behavior upon crystallization from solution. It consistently produces its stable form A with a uniform crystal size distribution on the surface of an Au(111) template while concomitantly forming its metastable form D within the same bulk solution. Molecular modeling using empirical atomistic force-fields reveals more complex molecular and intermolecular structures for form D compared to form A, with the crystal chemistry of both polymorphs being dominated by van der Waals and π-π stacking interactions with lower contributions (ca. 20%) from hydrogen bonding and electrostatic interactions. Comparative lattice energies and convergence for the polymorphs are consistent with the observed concomitant polymorphic behavior. Synthon characterization reveals an elongated needle-like morphology for form D crystals in contrast to the more equant form A crystals with the surface chemistry of the latter exposing the molecules' cyano groups on its {010} and {011} habit faces. Density functional theory modeling of surface adsorption reveals preferential interactions between Au and the synthon GA interactions of form A on the Au surface. Molecular dynamics modeling of the entacapone/gold interface reveals the entacapone molecular structure within the first adsorbed layer to show nearly identical interaction distances, for both the molecules within form A or D with respect to the Au surface, while in the second and third layers when entacapone molecule-molecule interactions overtake the interactions between those of molecule-Au, the intermolecular structures are found to be closer to the form A structure than form D. In these layers, synthon GA (form A) could be reproduced with just two small azimuthal rotations (5° and 15°) whereas the closest alignment to a form D synthon requires larger azimuthal rotations (15° and 40°). The cyano functional group interactions with the Au template dominate interfacial interactions with these groups being aligned parallel to the Au surface and with nearest neighbor distances to Au atoms more closely matching those in form A than form D. The overall polymorph direction pathway thus encompasses consideration of molecular, crystal, and surface chemistry factors.

Interaction between pentacene molecules and monolayer transition metal dichalcogenides.

Using first-principles calculations based on density-functional theory, we investigated the adsorption of pentacene molecules on monolayer two-dimensional transition metal dichalcogenides (TMD). We considered the four most popular TMDs, namely, MoS2, MoSe2, WS2 and WSe2, and we examined the structural and electronic properties of pentacene/TMD systems. We discuss how monolayer pentacene interacts with the TMDs, and how this interaction affects the charge transfer and work function of the heterostructure. We also analyse the type of band alignment formed in the heterostructure and how it is affected by molecule-molecule and molecule-substrate interactions. Such analysis is valuable since pentacene/TMD heterostructures are considered to be promising for application in flexible, thin and lightweight photovoltaics and photodetectors.

Influence of core size on self-assembled molecular networks composed of C3h-symmetric building blocks through hydrogen bonding interactions: structural features and chirality.

The effect of the core size on the structure and chirality of self-assembled molecular networks was investigated using two aromatic carboxylic acid derivatives with frameworks displaying C3h symmetry, triphenylene derivative H3TTCA and dehydrobenzo[12]annulene (DBA) derivative DBACOOH, each having three carboxy groups per molecule. Scanning tunneling microscopy observations at the 1-heptanoic acid/graphite interface revealed H3TTCA exclusively forming a chiral honeycomb structure, and DBACOOH forming three structures (type I, II, and III structures) depending on its concentration and whether the system is subjected to annealing treatment. Hydrogen bonding interaction patterns and chirality were carefully analyzed based on a modeling study using molecular mechanics simulations. Moreover, DBACOOH forms chiral honeycomb structures through the co-adsorption of guest molecules. Structural diversity observed for DBACOOH is attributed to its relatively large core size, with this feature modulating the balance between molecule-molecule and molecule-substrate interactions.

Growth of 1D ClAlPc molecular chains mediated by graphene moiré patterns.

The on-surface formation of iso-oriented 1D molecular architectures, with high structural perfection, on 2D materials has been a long-sought objective. However, such realization has been troublesome and limited, and it still remains an experimental challenge. Here, the quasi-1D stripe-like moiré pattern, arising at the interface of graphene grown on Rh(110), has been used to guide the formation of 1D molecular wires of π-conjugated, non-planar, chloro-aluminum phthalocyanine (ClAlPc) molecules, brought together by van der Waals interactions. Using scanning tunnelling microscopy (STM) under ultra-high vacuum (UHV) at 40 K, the preferential adsorption orientations of the molecules at low coverages have been investigated. The results shed light on the potential signature of graphene lattice symmetry breaking, induced by the incommensurate quasi-1D moiré pattern of Gr/Rh(110), as the subtle mechanism behind this templated growth of 1D molecular structures. For coverages close to 1 ML, the molecule-molecule interactions favor a closely packed square lattice arrangement. The present work provides new insights to tailor 1D molecular structures on graphene grown on a non-hexagonal metal substrate.

Coverage-modulated halogen bond geometry transformation in supramolecular assemblies.

Halogen bonding (HB) has emerged as a promising route for designing supramolecular assemblies due to its directional nature and versatility in modifying interactions through the choice of halogens and molecular entities. Despite this, methods for tuning these interactions on surfaces, particularly in terms of directionality, are limited. In this study, we present a strategy for tuning the directionality of self-assembly processes in homomolecular organic compounds on inert metal surfaces. A variety of halogen-halogen geometries can promote highly-extended one-dimensional or two-dimensional self-assembly depending on the molecular coverage. Our results indicate that under lower molecular coverage conditions, robust one-dimensional (1D) structures promote the self-assembly of halogen-bonded molecules on Au(111). At certain coverage, a transformation from type-I to synthon halogen bonding is observed, leading to an extended hexagonal pattern of molecular assembly. The atomistic details of the structures are experimentally studied using high-resolution atomic force microscopy and supported by first-principle calculations. We employed DFT to evaluate the interplay between electrostatics and dispersion forces driving both type-I and synthon assemblies. The results reveal a halogen-bond geometry transformation induced by a subtle balance of molecule-molecule interaction. Finally, we investigate the capability of the halogen-bonded supramolecular assembly to periodically confine electronic quantum states and single atoms. Our findings demonstrate the versatility of sigma-bonding in regulating molecular assembly and provide new insights for tailoring functional molecular structures on an inert metal substrate.

Circular RNA circPRDX3 mediates neuronal survival apoptosis in ischemic stroke by targeting miR-641 and NPR3

ObjectivecircPRDX3 is a circular RNA (circRNA) that has received little attention yet. The purpose of this research is to elucidate circPRDX3 expression pattern and its underlying network in ischemic stroke (IS). MethodsOxygen-glucose deprivation on/reoxygenation (OGD/R) and mice model of middle cerebral artery occlusion (MCAO) were used to generate IS model in N2a cells or mice, respectively. Expression levels of circPRDX3, miR-641, Natriuretic Peptide Receptor 3 (NPR3), and members of the mitogen-activated protein kinases (MAPK) pathway were determined using real-time quantitative PCR (qRT-PCR) and western blot. Cell viability was assessed by CCK-8 assay and apoptosis was evaluated using TUNEL staining and flow cytometry. Molecule-molecule interactions were verified by dual luciferase and RNA immunoprecipitation (RIP) assays. The infarcted area was depicted by Triphenyl tetrazolium chloride (TTC) staining and the level of neurological function was measured using National Institute of Health stroke scale (NIHSS). ResultsCircPRDX3 and NPR3 were shown to be considerably downregulated in IS samples, as well as OGD/R cells or MCAO mice, while miR-641 was found to be significantly upregulated. A circPRDX3/miR-641/NPR3 mechinary was verified using luciferase and RIP assays. Overexpression of circPRDX3 dramatically reduced miR-641 expression and increased NPR3 expression, boosting cell survival and lowering apoptosis in an OGD/R model, either with inactivated MAPK signaling pathways. Moreover, overexpression of circPRDX3 lowered infarct volume and enhanced neurobehavioral outcomes in mice after MCAO, and these protective effects were dramatically abrogated by depletion of NPR3. ConclusionAltogether, circPRDX3 inhibited the development of IS by sponging miR-641, hence increasing NPR3 expression and inactivating MAPK pathway. These results may aid in the search of potential therapy targets for IS.

On the Possibility of Exploring Tip-Molecule Interactions with STM Experiments

We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions by using the same methodology. Explicit results are derived for an harmonic attractive and repulsive tip-molecule interaction. Applications of the theory allows one to estimate the type and strength of interactions between the STM tip and the molecule. This includes the possibility of an estimation of molecule-molecule interaction when the tip is decorated by a molecule. Despite our focus on STM, this theory can analogously be applied to other experimental probes that monitor single molecules.

(Digital Presentation) Carbon Quantum Dot Assisted Enhancement of S2 Fluorescence of Near-Infrared Dyes through Immobilization-Induced Emission Effect

Aggregation-induced emission of organic dyes is a phenomenon in which organic luminophores show higher photoluminescence (PL) efficiency in the aggregated state than in a free molecule, due to the freezing rotational degrees of freedom of the luminophore which otherwise quench the PL emission. In many cases, however, coupling of molecules leads to quenching of their emission due to the concentration quenching or self-quenching (exciton-exciton annihilation) effect. Therefore, in order to realize an enhanced PL emission as a result of molecule-molecule interaction a fine balance should be achieved between freezing rotational degrees of freedom of the molecule and escaping self-quenching effect. This could be realized via immobilization of the luminophore onto the inert surface.Here, we demonstrate an enhancement of specific S2 emission of the near-infrared (NIR) dyes of tricarbocyanine family due to their immobilization on the surface of carbon nanoparticles that induce freezing a specific planar conformation of the molecule imposed by the carbon plane of the particle it interact with. Carbon quantum dots serve as inert particles that render an opposite influence on the S1 and S2 emission of the tricarbocyanine dyes. We demonstrate a dual emission of the NIR tricarbocyanine dyes with a bright green S2 fluorescence, which is relatively weak for the free dye molecule but whose quantum yield increases by 2-4 times, together with a strong enhancement of the spontaneous rate of S2 fluorescence, whereas the quantum yield of S1 emission in the NIR decreases by 2-7 times, respectively, as a result of immobilization of the dye molecule via the interaction with carbon quantum dots. The above changes are dependent on the terminal and meso-groups of the dye and the solvent used. The dye immobilization due to interaction with carbon quantum dots causes freezing rotational degrees of freedom of the molecule as indicated by suppression of the dye hot band absorption-assisted anti-Stokes S1 emission.The observed “lighting up” of an anti-Kasha emission, i.e., the emission from Sn (n>1) excited levels, of the NIR chromophores which possess intensive S1 absorption and emission in the NIR region, but which are spectrally silent in the visible, can lead to their potential applications in the fields such as energy conversion, bio-imaging and bio-sensing, sensitization of solar cells, etc.

Efficient modeling of organic adsorbates on oxygen-intercalated graphene on Ir(111)

Organic charge transfer complexes (CTCs) can be grown as thin films on intercalated graphene (Gr). Deciphering their precise film morphologies requires global ab initio structure search, where configurational sampling is computationally intractable unless we reconsider the model for the complex substrate. In this study, we employ charged freestanding Gr to approximate an intercalated Gr/O/Ir(111) substrate, without altering the adsoption properties of deposited molecules. We compare different methods of charging Gr and select the most appropriate substitute model for Gr/O/Ir(111) that maintains the adsorption properties of fluorinated tetracyanoquinodimethane (${\mathrm{F}}_{4}\mathrm{TCNQ}$) and tetrathiafulvalene (TTF), prototypical electron acceptor/donor molecules in CTCs. Next, we apply our model in the Bayesian optimization structure search method and density-functional theory to identify the stable structures of ${\mathrm{F}}_{4}\mathrm{TCNQ}$ and TTF on supported Gr. We find that both molecules physisorb to Gr in various configurations. The narrow range of adsorption energies indicates that the molecules may diffuse easily on the surface and molecule-molecule interactions likely have a central role in film formation. Our study shows that complex intercalated substrates may be approximated with charged freestanding Gr, which can facilitate exhaustive structure search of CTCs.

On-Surface Reactivity of Disubstituted-Bianthryl Molecules on Cu(111) and Au(111) Surfaces

On-surface π-conjugated 1D polymers, like graphene nanoribbons, have emerged as a class of promising materials. On-surface chemical properties of 9,9′-bianthryl molecules are widely developed as they can be used as starting building blocks to provide graphene nanoribbons. Here, we propose to investigate the chemical behavior of 10,10′-disubstituted-9,9′-bianthryl molecules on Cu(111) and Au(111) surfaces by using scanning tunneling microscopy under ultra-high vacuum. We demonstrated that the balance between molecule-molecule interaction, molecule-substrate interaction, and molecular rearrangement, drastically alter the chemical properties of the adsorbed molecule by thermal annealing.

Beyond the Molecule: Intermolecular Forces from Gas Liquefaction to X-H⋅⋅⋅π Hydrogen Bonds.

Interest toward molecule-molecule interactions developed during the first half of the 19th century with studies on gas liquefaction. In 1869, Andrews carried out the first accurate study on the effects of temperature and pressure on the behaviour of real gases, and in 1873, van der Waals formulated an equation capable of accounting for critical phenomena of each individual gas The nature of the intermolecular forces responsible for aggregation of gases was investigated in the early 20th century by Keesom and Debye (electrostatic interactions between dipoles) and by London (interaction between instantaneous dipoles, studied by quantum mechanics). The hydrogen bond theory, a particular case of dipolar interaction, originated in the 1920s in Berkeley in the institute directed by G. N. Lewis. Later it was made clear that hydrogen bonding is responsible for the aggregation of most biological systems, from proteins to nucleic acids. This Perspective describes the most significant steps through which the science of intermolecular interactions has progressed over the last two centuries, revisiting classical experiments and theoretical formulations, which led to the complex state of art of today.

On-Surface Synthesis of Ligands to Elaborate Coordination Polymers on an Au(111) Surface.

On-surface metal-organic polymers have emerged as a class of promising 2D materials. Here, we propose a new strategy to obtain coordination polymers by transforming supramolecular networks into coordination polymers by surface-assisted cyclo-dehydrogenation of organic building blocks. All nanostructures are fully characterized by using scanning tunneling microscopy under ultra-high vacuum on a gold surface. We demonstrated that the balance between molecule-molecule interaction and molecule-substrate interaction can be drastically modified by a strong modification of the geometry of the molecules thanks to a thermal annealing. This new way is an efficient method to elaborate on-surface coordination polymers.

Long-range strength and anisotropies of molecule-molecule interactions: Ab initio calculations, spherical harmonics expansions, and the second virial coefficient for the [formula omitted] gaseous mixture

The analytical representation of intermolecular interactions combines dynamical and structural viewpoints, utilizing a spherical harmonics expansion based on high-level ab initio generated stereodirected configurations. The potential energy surface of the H2⋯F2 system is built by a number of selected cuts (leading configurations); the best fits of their dependence on the intermolecular distance are phenomenologically represented by the Pirani et al. potential functions. The quality of the representation is validated by accurate calculations of a property of the gaseous mixture, the second virial coefficient, in a range of temperatures. Convergence is demonstrated by comparison with elaborate semiempirical approaches.