Interionic potentials for alkali halides. II. Completely crystal independent specification of Born-Mayer potentials

Forecasting the Pharmacological Mechanisms of Plumbago zeylanica and Solanum xanthocarpum in Diabetic Retinopathy Treatment: A Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Study

(1) Background: Diabetic retinopathy (DR) is a major complication of diabetes, marked by abnormal angiogenesis, microaneurysms, and retinal hemorrhages. Traditional Ayurvedic medicine advocates multi-target strategies for DR management. However, the mechanisms by which Solanum xanthocarpum (SX) and Plumbago zeylanica (PZ) exert therapeutic effects are not well understood; (2) Methods: To investigate these mechanisms, we employed network pharmacology and molecular docking techniques. Phytochemicals from SX and PZ were identified using the IMPPAT database and Swiss Target Prediction tool. DR-related protein targets were sourced from the GeneCards database, and common targets were identified through Venn diagram analysis. STRING and Cytoscape were used to construct and analyze protein-protein interaction networks. Pathway enrichment was performed with Gene Ontology and KEGG databases; (3) Results: We identified 28 active phytoconstituents, targeting proteins such as EGFR, SRC, STAT3, AKT1, and HSP90AA1. Molecular docking and dynamics simulations confirmed the strong binding affinities of these compounds to their targets; (4) Conclusions: The study highlights the multi-target activity of SX and PZ, particularly in pathways related to EGFR tyrosine kinase inhibitor resistance and PI3K-AKT signaling. These findings provide valuable insights into their therapeutic potential for DR, suggesting the effective modulation of key molecular pathways involved in the disease.

Fluorescent nano-sized aggregates of halogen bonded complexes formed using perfluoropropyl iodides: a systematic comparison between two isomeric halogen bond acceptors, aniline and 4-methyl pyridine

The halogen bonds (XB) formed by the two isomers 4-methyl pyridine (MePy) and aniline (ANL) with heptafluoro-1-propyl iodide (n-C₃F₇I) and heptafluoro-2-propyl iodide (iso-C₃F₇I) were investigated using vibrational (FT-IR and Raman) spectroscopy and quantum mechanical calculations. While these two isomers indicated a distinctive impact on the ring related vibrations, molecular electrostatic potential, frontier molecular orbitals, intermolecular electron density delocalisation and consequential charge transfer upon halogen bonding with n-C₃F₇I and iso-C₃F₇I, the dramatic intermolecular charge transfer (CT) occurring on the MePy involved XB systems demonstrated an ion-pair like aggregation. Such aggregation, after 72 h and longer after mixing, leads to an emission of fluorescence for both [MePy·C₃F₇I] systems. The resulting nano-sized aggregates were characterised using UV-Vis absorption and fluorescence spectroscopy along with scanning and transmittance electron microscopy (SEM and TEM), wherein, the XB complex with iso-C₃F₇I showed a faster and more severe aggregation due to a stronger CT than that with n-C₃F₇I. The present work is the first case of aggregation induced emission (AIE) due to aggregation of XB complexes formed by small neutral molecules.

Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G4C2) repeat expansion in vitro and in vivo ALS models

[Figure: see text].

Role of tip apices in scanning force spectroscopy on alkali halides at room temperature-chemical nature of the tip apex and atomic-scale deformations

We have revealed processes of the tip apex distortion in the measurements of non-contact scanning force microscopy. High-spatial-resolution two-dimensional force mapping on KCl(100) surfaces for a large number of tips, seven tips, enabled us to see the complex behavior of the tip apex distortion. The tips are from Si without additional coating, but are altered by the tip-sample interaction and show the behavior of different atomic species. On the KCl(001) surfaces, the tip apex, consisting of K and Cl atoms or of Si, distorted several times while changing the distance even in a weak attractive region. There are variations in rigidity of the tip apex, but all tips distorted in the small attractive region. This complex behavior was categorized in patterns by our analyses. We compare the experimental force-distance data to atomistic simulations using rigid KCl-terminated tips and KCl-terminated tips with an additional KCl-pair designed to perform atomic jumps. We also compare the experimental force-distance data to first principles simulations using Si tips. We mainly find K-terminated tips and Si-terminated tips. We find that Si tips show only one force minimum whereas KCl-terminated tips show two force minima in line with the stronger rigidity of Si compared to KCl. At room temperature, the tip apex atoms can perform atomic jumps that change the atomic configuration of the tip apex.

New accurate molecular dynamics potential function to model the phase transformation of cesium lead triiodide perovskite (CsPbI3)

Inorganic metallic halide perovskites and cesium lead triiodide, CsPbI₃, in particular, have gained enormous attention recently due to their unique photovoltaic properties and low processing temperatures. However, their structural stability and phase transition still need an in-depth investigation to better optimize their optoelectronic properties. For sake of time and cost, Classical Molecular Dynamics (CMD) and first principles calculations are being used to predict the structure stability and phase transition of CsPbI₃. The major challenge of CMD is the choice of proper interatomic potential functions. In this paper, a new hybrid force field is being introduced, which integrates the embedded atomic potentials of Cs-Cs and Pb-Pb with Buckingham-Coulomb potentials. The Buckingham-Coulomb interatomic potential was solely employed as well. The outputs from both force fields were reported and compared to the experimental values. In fact, the new Hybrid Embedded Atomic Buckingham-Coulomb (EABC) potential reproduces, with a great degree of accuracy (within 2.5%), the structural properties, such as the radial distribution functions, interatomic separation distances, and the density. Also, it detects the phase transformation from an orthorhombic into a cubic crystal structure and the melting temperature at 594 K and 750 K respectively which agrees with the experimental values to within 1%. The new proposed hybrid potential proved to be accurate so it could potentially be used to infer the structure stability and the mechanical and thermal properties of the pure inorganic halide perovskites and the mixed halide perovskites as well which are used in various applications.

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.

Size does matter: how to control organization of organic dyes in aqueous environment using specific ion effects

Understanding the role played by external factors on the organization of molecules has the potential to contribute greatly to fundamental research and applications in fields as diverse as nanotechnology, medicine, material chemistry, etc. Countless studies involve the organization of small organic molecules in environments rich in ionic species, yet their participation in molecular organization is often overlooked. Herein, we critically assess the organization in aqueous solution of the cationic cyanine dye, thiazole orange, in the presence of different monovalent sodium salts. Our findings clearly indicate that not all ions are identical with regards to the organization of thiazole orange molecules and specific ions effects are at play. The conventional Debye and Hückel model is not sufficient to explain our results, and the participation of ionic species in molecular organization is explained in terms of the recent theory of water matching affinity. Herein, by choosing the right counterion with the appropriate size, we have shown that it is possible to either induce a simple shift in the monomer-dimer equilibrium of thiazole orange or to turn on the formation of larger organized structures.

Measuring electric field induced subpicometer displacement of step edge ions

We provide unambiguous evidence that the applied electrostatic field displaces step atoms of ionic crystal surfaces by subpicometers in different directions via the measurement of the lateral force interactions by bimodal dynamic force microscopy combined with multiscale theoretical simulations. Such a small imbalance in the electrostatic interaction of the shifted anion-cation ions leads to an extraordinary long-range feature potential variation and is now detectable with the extreme sensitivity of the bimodal detection.

The role of the tip in non-contact atomic force microscopy dissipation images of ionic surfaces

In this paper we use simulations to investigate the role of the tip in nc-AFM measurements of dissipated energy. Using a virtual AFM we simulate the experiment focusing on the atomic scale energy dissipation on an NaCl(100) flat surface. The non-conservative interaction was treated with the theory of dynamic response and all the calculations were carried out using an atomistic model; several sets of tips were tested using ionic crystals (NaCl, KBr, MgO), each in different configurations (ideal, vacant, divacant, doped). Using an MgO-doped tip we were able to calculate a dissipation signal comparable to what is typically measured in experiments. It was not possible to see any dissipation with ideal tips, although they still have a significant interaction with the surface and give atomic contrast in the frequency shift signal. The effect of the scanning speed on measured frequency shift and dissipation is also calculated and discussed.

An introduction to “Computational Crystallography”

The currently available methods for the computation of structures and their properties are reviewed. After a brief introduction into some common technical aspects, the capabilities and limitations of the most commonly used approaches are discussed. Examples are given to show the state of the art in Computational “Crystallography”, and possible future developments are outlined

Site-specific force-vector field studies of KBr(001) by atomic force microscopy

The spatial orientation and magnitude of forces acting between the tip atoms of an atomic force microscope tip and the surface atoms of an atomically clean surface can be determined by force field measurements. We compare two force-vector fields obtained along and between the ionic lattice sites of a KBr(001) surface with atomistic simulations for two differently configured tips. This careful analysis allows us to identify the K(+)-termination of the tip apex as well as the polarity of the KBr lattice.

Atomic-scale force-vector fields

The magnitude and direction of forces acting between individual atoms as a function of their relative position can be described by atomic-scale force-vector fields. We present a noncontact atomic force microscopy based determination of the force fields between an atomically sharp tip and the (001) surface of a KBr crystal in conjunction with atomistic simulations. The direct overlap of experiment and simulation allows identification of the frontmost tip atom and of the surface sublattices. Superposition of vertical and lateral forces reveals the spatial orientation of the interatomic force vectors.

Dynamic Intensity Model Calculation of Vibronic Oscillator Strengths for Cs2NaNdCl6: A Molecular Dynamics Study

We present here a dynamic intensity model calculation of vibronic oscillator strengths for the Cs2NaNdCl6 compound by applying the method of molecular-dynamics simulation (MDS). The force field parameters used for the MDS reproduce the structure and several vibrational frequencies of Cs2NaNdCl6 very well. Both the static-coupling (SC) and dynamic-coupling (DC) mechanisms are taken into account for the intensity parameter calculations, in which the effective point charges and isotropic polarizabilities are optimized with respect to experimental energy levels. A comparison of intensity parameters and vibronic oscillator strengths between the two individual mechanisms indicates that the DC mechanism is operative. The calculated vibronic oscillator strengths for the combined SC and DC mechanism agree quite well with the available experimental values.

Sublattice identification in scanning force microscopy on alkali halide surfaces

We propose and apply to the KBr(001) surface a new procedure for species recognition in scanning force microscopy (SFM) of ionic crystal surfaces which show a high symmetry of the charge arrangement. The method is based on a comparison between atomistic simulations and site-specific frequency versus distance measurements. First, by taking the difference of force-distance curves extracted at a few judiciously chosen surface sites we eliminate site-independent long-range forces. The obtained short-range force differences are then compared with calculated ones assuming plausible tip apex models. This procedure allows for the first time identification of the tip apex polarity and of the positive and negative sublattices in SFM images of the (001) cleavage surface of an ionic crystal with the rock salt structure.

Many-body potentials for aqueous Li+, Na+, Mg2+, and Al3+: Comparison of effective three-body potentials and polarizable models

Many-body potentials for the aqueous Li(+), Na(+), Mg(2+), and Al(3+) ions have been constructed from ab initio cluster calculations. Pure pair, effective pair, effective three-body, and effective polarizable models were created and used in subsequent molecular dynamics simulations. The structures of the first and second solvation shells were studied using radial distribution functions and angular-radial distribution functions. The effective three-body and polarizable potentials yield similar first-shell structures, while the contraction of the O-O distances between the first and second solvation shells is more pronounced with the polarizable potentials. The definition of the tilt angle of the water molecules around the ions is discussed. When a proper definition is used, it is found that for Li(+), Mg(2+), and Al(3+) the water molecules prefer a trigonal orientation, but for Na(+) a tetrahedral orientation (ion in lone-pair direction) is preferred. The self-diffusion coefficients for the water molecules and the ions were calculated; the ionic values follow the order obtained from experiment, although the simulated absolute values are smaller than experiment for Mg(2+) and Al(3+).

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.