Molecular Structure Research Articles

CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages.

Organic(porous) and metal-organic cages are promising biomimetic platforms with diverse applications spanning recognition, sensing, and catalysis. The key to the emergence of these functions is the presence of well-defined inner cavities capable of binding a wide range of guest molecules and modulating their properties. However, despite the myriad cage architectures currently available, the rational design of structurally diverse and functional cages with specific host-guest properties remains challenging. Efficiently predicting such properties is critical for accelerating the discovery of novel functional cages. Herein, we introduce CageCavityCalc (C3), a Python-based tool for calculating the cavity size of molecular cages. The code is available on GitHub at https://github.com/VicenteMartiCentelles/CageCavityCalc. C3 utilizes a novel algorithm that enables the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. Moreover, C3 facilitates easy visualization of the computed cavity size alongside hydrophobic and electrostatic potentials, providing insights into host-guest interactions within the cage. Furthermore, the calculated cavity can be visualized using widely available visualization software, such as PyMol, VMD, or ChimeraX. To enhance user accessibility, a PyMol plugin has been created, allowing nonspecialists to use this tool without requiring computer programming expertise. We anticipate that the deployment of this computational tool will significantly streamline cage cavity calculations, thereby accelerating the discovery of functional cages.

A Novel Family of Luminescent Pyrenyl‐(N‐Heterocyclic Carbene)‐ Halogenated Coinage Metal Complexes: Synthesis, Crystal Structures, and Optical Properties

A family of luminescent pyrenyl‐(NHC)‐M‐Cl coinage metal complexes has been prepared and fully characterized (NHC = N‐heterocyclic carbene). Two classes of complexes are described: (M = Cu (1a), Ag (2a), Au (3a) where pyrenyl‐(NHC) = 1‐pyrenyl‐3‐methyl‐Imidazolin‐2‐ylidene and M = Cu (1b), Ag (2b), Au (3b) with pyrenyl‐(NHC) = 1‐pyrenyl‐3‐naphthyl‐Imidazolin‐2‐ylidene. The molecular structures of the six complexes were confirmed by single crystal X‐ray diffraction studies. All complexes were found to be emissive in solution and solid state. The use of the chromophoric‐(NHC) ligand endows to these complexes emissive properties in solution in the blue region (376‐397nm). The presence of the naphthyl‐substituent in the 1b‐3b series enhances the quantum yields relative to the methyl‐series 1a‐3a. In particular, the carbene gold complexes were the most emissive and displayed the highest quantum yields

Structural, Vibrational Spectroscopic and Theoretical (DFT) Studies of 4-Chloro- and 5-Chloro-7-azaindole-3-carbaldehydes

Molecular structures of 5-chloro-7-azaindole-3-carbaldehyde (5Cl7AICA) and 4-chloro-7-azaindole-3-carbaldehyde (4Cl7AICA) were investigated using infrared and Raman spectroscopy supported by density functional theory (DFT) calculations. Theoretical studies were carried out with three DFT methods, which include dispersion corrections: B3LYP-D3, PBE0-D3, and ωB97X-D. A single-crystal X-ray diffraction analysis was performed for 5Cl7AICA. The compound crystallizes in the monoclinic system, space group P21/c, with lattice parameters a = 3.82810(12) Å, b = 12.7330(3) Å, c = 15.9167(5) Å, and β = 94.539(3)°, with Z = 4. Within the crystal lattice, 5Cl7AICA molecules form dimers via dual and strong N1–H1⋅⋅⋅N7′ hydrogen bonds, accompanied by other intermolecular interactions. In the DFT calculations, two types of dimers of the investigated molecules were analyzed: dimer 1, which is present in the crystal structure of 5Cl7AICA, and dimer 2 displaying a 180° rotation of the aldehyde group compared to dimer 1. Computational results indicate that dimer 1 is more stable than dimer 2 for 5Cl7AICA, whereas dimer 2 is more stable than dimer 1 for 4Cl7AICA molecules. Furthermore, experimental and theoretical vibrational spectra were examined to elucidate the influence of internal rotation of the aldehyde group on spectroscopic properties.

Graph Neural Networks in Point Clouds: A Survey

With the advancement of 3D sensing technologies, point clouds are gradually becoming the main type of data representation in applications such as autonomous driving, robotics, and augmented reality. Nevertheless, the irregularity inherent in point clouds presents numerous challenges for traditional deep learning frameworks. Graph neural networks (GNNs) have demonstrated their tremendous potential in processing graph-structured data and are widely applied in various domains including social media data analysis, molecular structure calculation, and computer vision. GNNs, with their capability to handle non-Euclidean data, offer a novel approach for addressing these challenges. Additionally, drawing inspiration from the achievements of transformers in natural language processing, graph transformers have propelled models towards global awareness, overcoming the limitations of local aggregation mechanisms inherent in early GNN architectures. This paper provides a comprehensive review of GNNs and graph-based methods in point cloud applications, adopting a task-oriented perspective to analyze this field. We categorize GNN methods for point clouds based on fundamental tasks, such as segmentation, classification, object detection, registration, and other related tasks. For each category, we summarize the existing mainstream methods, conduct a comprehensive analysis of their performance on various datasets, and discuss the development trends and future prospects of graph-based methods.

Pharmacological actions of the bioactive compounds of Epimedium on the male reproductive system: current status and future perspective.

Compounds isolated from Epimedium include the total flavonoids of Epimedium, icariin, and its metabolites (icaritin, icariside I, and icariside II), which have similar molecular structures. Modern pharmacological research and clinical practice have proved that Epimedium and its active components have a wide range of pharmacological effects, especially in improving sexual function, hormone regulation, anti-osteoporosis, immune function regulation, anti-oxidation, and anti-tumor activity. To date, we still need a comprehensive source of knowledge about the pharmacological effects of Epimedium and its bioactive compounds on the male reproductive system. However, their actions in other tissues have been reviewed in recent years. This review critically focuses on the Epimedium, its bioactive compounds, and the biochemical and molecular mechanisms that modulate vital pathways associated with the male reproductive system. Such intrinsic knowledge will significantly further studies on the Epimedium and its bioactive compounds that protect the male reproductive system and provide some guidances for clinical treatment of related male reproductive disorders.

Structural, Vibrational Spectroscopic and Theoretical (DFT) Studies of 4-Chloro- and 5-Chloro-7-azaindole-3-carbaldehydes

Molecular structures of 5-chloro-7-azaindole-3-carbaldehyde (5Cl7AICA) and 4-chloro-7-azaindole-3-carbaldehyde (4Cl7AICA) were investigated using infrared and Raman spectroscopy supported by density functional theory (DFT) calculations. Theoretical studies were carried out with three DFT methods, which include dispersion corrections: B3LYP-D3, PBE0-D3, and ωB97X-D. A single-crystal X-ray diffraction analysis was performed for 5Cl7AICA. The compound crystallizes in the monoclinic system, space group P21/c, with lattice parameters a = 3.82810(12) Å, b = 12.7330(3) Å, c = 15.9167(5) Å, and β = 94.539(3)°, with Z = 4. Within the crystal lattice, 5Cl7AICA molecules form dimers via dual and strong N1–H1⋅⋅⋅N7′ hydrogen bonds, accompanied by other intermolecular interactions. In the DFT calculations, two types of dimers of the investigated molecules were analyzed: dimer 1, which is present in the crystal structure of 5Cl7AICA, and dimer 2 displaying a 180° rotation of the aldehyde group compared to dimer 1. Computational results indicate that dimer 1 is more stable than dimer 2 for 5Cl7AICA, whereas dimer 2 is more stable than dimer 1 for 4Cl7AICA molecules. Furthermore, experimental and theoretical vibrational spectra were examined to elucidate the influence of internal rotation of the aldehyde group on spectroscopic properties.

Review of the Interfacial Structure and Properties of Surfactants in Petroleum Production and Geological Storage Systems from a Molecular Scale Perspective.

Surfactants play a crucial role in tertiary oil recovery by reducing the interfacial tension between immiscible phases, altering surface wettability, and improving foam film stability. Oil reservoirs have high temperatures and high pressures, making it difficult and hazardous to conduct lab experiments. In this context, molecular dynamics (MD) simulation is a valuable tool for complementing experiments. It can effectively study the microscopic behaviors (such as diffusion, adsorption, and aggregation) of the surfactant molecules in the pore fluids and predict the thermodynamics and kinetics of these systems with a high degree of accuracy. MD simulation also overcomes the limitations of traditional experiments, which often lack the necessary temporal-spatial resolution. Comparing simulated results with experimental data can provide a comprehensive explanation from a microscopic standpoint. This article reviews the state-of-the-art MD simulations of surfactant adsorption and resulting interfacial properties at gas/oil-water interfaces. Initially, the article discusses interfacial properties and methods for evaluating surfactant-formed monolayers, considering variations in interfacial concentration, molecular structure of the surfactants, and synergistic effect of surfactant mixtures. Then, it covers methods for characterizing microstructure at various interfaces and the evolution process of the monolayers' packing state as a function of interfacial concentration and the surfactants' molecular structure. Next, it examines the interactions between surfactants and the aqueous phase, focusing on headgroup solvation and counterion condensation. Finally, it analyzes the influence of hydrophobic phase molecular composition on interactions between surfactants and the hydrophobic phase. This review deepened our understanding of the micro-level mechanisms of oil displacement by surfactants and is beneficial for screening and designing surfactants for oil field applications.

Amesp: Atomic and molecular electronic structure program

The atomic and molecular electronic structure program (Amesp) is a general-purpose electronic structure program designed for the study of molecular electronic structures. It incorporates a series of modern electronic structure methods, including Hartree–Fock, density functional theory, Multiconfigurational self-consistent field, Møller–Plesset, configuration-interaction, coupled-cluster, semiempirical methods, and molecular force fields. Amesp strives to offer an efficient and user-friendly tool specifically designed for computing for molecules ranging from small to complex biomolecules. In this paper, we highlight the features of Amesp and offer an overview.

First-principles Study of Phase-dependent Carrier Transport Mechanism for MASnI3 Sn-based Halide Perovskite.

Organic-inorganic hybrid perovskites have attracted tremendous attentions owing to their excellent properties as next-generation photovoltaic devices. With soft covalent framework, organic-inorganic hybrid perovskites exhibit different phases at different temperatures. The band-edge features of perovskites are mainly contributed by inorganic framework, which means the structural differences between these phases would lead to complex carrier transport. We investigated the carrier transport of Sn-based organic-inorganic hybrid perovskite CH3NH3SnI3 (MASnI3), considering acoustic deformation potential scattering, ionized impurity scattering, and polar optical phonon scattering. It is found that the electron mobility of each phase of MASnI3 is strongly correlated with the Sn-I-Sn bond angle and there is in-plane/out-of-plane anisotropy. The pCOHP (projected crystal orbital Hamilton population) analysis suggested that the tilt and rotation of the [SnI6]4- octahedron influence the Sn(p)-I(p) orbital electron coupling and the electron transport, leading to different band-edge features in multiple phases. The carrier mobility with respect to temperature was further calculated for each phase of MASnI3 in respective temperature intervals, showing lower carrier mobility in high temperature. Comparing the contribution of different scattering mechanisms, it was found that the dominant scattering mechanism is polar optical phonon scattering, while multiple scattering mechanisms compete in individual cases.

Rapid Estimation of the Intermolecular Electronic Couplings and Charge-Carrier Mobilities of Crystalline Molecular Organic Semiconductors through a Machine Learning Pipeline.

Organic semiconductors (OSC) offer tremendous potential across a wide range of (opto)electronic applications. OSC development, however, is often limited by trial-and-error design, with computational modeling approaches deployed to evaluate and screen candidates through a suite of molecular and materials descriptors that generally require hours to days of computational time to accumulate. Such bottlenecks slow the pace and limit the exploration of the vast chemical space comprising OSC. When considering charge-carrier transport in OSC, a key parameter of interest is the intermolecular electronic coupling. Here, we introduce a machine learning (ML) model to predict intermolecular electronic couplings in organic crystalline materials from their three-dimensional (3D) molecular geometries. The ML predictions take only a few seconds of computing time compared to hours by density functional theory (DFT) methods. To demonstrate the utility of the ML predictions, we deploy the ML model in conjunction with mathematical formulations to rapidly screen the charge-carrier mobility anisotropy for more than 60,000 molecular crystal structures and compare the ML predictions to DFT benchmarks.

Enhancing photocatalytic hydrogen production in conjugated porous polymers through donor-π-donor fragment insertion

Recent progress in conjugated polymer photocatalysts has opened avenues for enhancing photocatalytic hydrogen production (PHP) activity through structural design. This study highlights the impact of the acceptor-to-donor feed ratio on PHP activity in copolymers, influencing their energy level structures. Five conjugated porous polymers (CPPs) were synthesized by adjusting the acceptor-to-donor molar ratio. Notably, at a 2:1 acceptor-to-donor ratio, the polymer demonstrated a high hydrogen evolution rate (HER) of 61.9 mmol g−1 h−1 under full arc irradiation without co-catalysts and an apparent quantum yield (AQY) of 7.77% at 475 nm. However, further increasing the proportion of the donor unit in the copolymers decreases their HER. Experiments and theoretical simulation characterized that the feed ratios effectively tune the polymer's molecular structure, hydrophilicity, band gap, and the generation and transport efficiency of photo-induced charge carriers, ultimately affecting the hydrogen production kinetics and efficiency. This research demonstrates that tuning the band structure and chemical compositions of CPPs through statistical copolymerization significantly impacts their PHP activity.

Enhancing photocatalytic hydrogen production in conjugated porous polymers through donor-π-donor fragment insertion

Recent progress in conjugated polymer photocatalysts has opened avenues for enhancing photocatalytic hydrogen production (PHP) activity through structural design. This study highlights the impact of the acceptor-to-donor feed ratio on PHP activity in copolymers, influencing their energy level structures. Five conjugated porous polymers (CPPs) were synthesized by adjusting the acceptor-to-donor molar ratio. Notably, at a 2:1 acceptor-to-donor ratio, the polymer demonstrated a high hydrogen evolution rate (HER) of 61.9 mmol g−1 h−1 under full arc irradiation without co-catalysts and an apparent quantum yield (AQY) of 7.77% at 475 nm. However, further increasing the proportion of the donor unit in the copolymers decreases their HER. Experiments and theoretical simulation characterized that the feed ratios effectively tune the polymer's molecular structure, hydrophilicity, band gap, and the generation and transport efficiency of photo-induced charge carriers, ultimately affecting the hydrogen production kinetics and efficiency. This research demonstrates that tuning the band structure and chemical compositions of CPPs through statistical copolymerization significantly impacts their PHP activity.

Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies.

The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.

Construction of macromolecular structure model of Luling coal and study on the dynamic mechanism of micro-wetting process

The physicochemical structure and energy composition of coal macromolecules are the major factors affecting coal wettability. This study thus employed 13C NMR, FTIR, and XPS to determine the chemical structure of coal in the No. 10 coal seam of the Luling coal mine and gain insights into the molecular mechanisms of coal wetting. The results showed that the molecular formula of the Luling 10 model was C290H223O25N5S. Through molecular dynamics simulation, upon the stable adsorption of sodium dodecyl sulfate (SDS) on the coal surface, both the mobility of water molecules and the water molecule content in the interfacial adsorption layer increased. After SDS was added, except for the hydrogen bond energy, the increase rate of each potential energy increased, and van der Waals energy and bond length energy changed the most. The reason for the decrease of hydrogen bond energy is that more atoms in coal macromolecules form hydrogen bonds with polar water molecules. The increase of SDS promoted the significant changes of bond length energy, bond angle energy and van der Waals force of coal, thus increasing the wettability of coal. Taken together, our findings provide important insights into the molecular mechanisms through which surfactants improve chemical wetting.

Half-Sandwich Iridium Complexes: A Recyclable and Stable Catalyst for Dehydrogenation of Alcohols to Carboxylic Acids.

A series of acylhydrazone-based N,N-chelate half-sandwich iridium complexes have been synthesized through a facile route in good yields. The dehydrogenation of a series of aromatic and aliphatic primary alcohols to corresponding carboxylic acids has been accomplished catalyzed by the prepared air stable iridium complexes under mild reaction conditions. Carboxylic acids were obtained in high yields under open flask condition with broad substrates and good tolerance to sensitive functional groups. Such a half-sandwich iridium catalyst system exhibited high catalytic activity and stability, and a high TOF of 316.7 h-1 could be achieved with a catalyst loading as low as 0.05 mol %. Furthermore, the sustainable catalyst could be reused at least five times without obviously losing its activity, highlighting its potential application in industry. Molecular structure of iridium complex 1 was confirmed by single-crystal X-ray analysis.

Interfacial Water Is Separated from a Hydrophobic Silica Surface by a Gap of 1.2 nm.

The interaction of liquid water with hydrophobic surfaces is ubiquitous in life and technology. Yet, the molecular structure of interfacial liquid water on these surfaces is not known. By using a 3D atomic force microscope, we characterize with angstrom resolution the structure of interfacial liquid water on hydrophobic and hydrophilic silica surfaces. The combination of 3D AFM images and molecular dynamics simulations reveals that next to a hydrophobic silica surface, there is a 1.2 nm region characterized by a very low density of water. In contrast, the 3D AFM images obtained of a hydrophilic silica surface reveal the presence of hydration layers next to the surface. The gap observed on hydrophobic silica surfaces is filled with two-to-three layers of straight-chain alkanes. We developed a 2D Ising model that explains the formation of a continuous hydrocarbon layer on hydrophobic silica surfaces.

Epigallocatechin gallate and curcumin inhibit Bcl-2: a pharmacophore and docking based approach against cancer.

The protein Bcl-2, well-known for its anti-apoptotic properties, has been implicated in cancer pathogenesis. Identifying the primary gene responsible for promoting improved cell survival and development has provided compelling evidence for preventing cellular death in the progression of malignancies. Numerous research studies have provided evidence that the abundance of Bcl-2 is higher in malignant cells, suggesting that suppressing Bcl-2 expression could be a viable therapeutic approach for cancer treatment. In this study, we acquired a compound collection using a database that includes constituents from Traditional Chinese Medicine (TCM). Initially, we established a pharmacophore model and utilized it to search the TCM database for potential compounds. Compounds with a fitness score exceeding 0.75 were selected for further analysis. The Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis identified six compounds with favorable therapeutic characteristics. The compounds that successfully passed the initial screening process based on the pharmacodynamic model were subjected to further evaluation. Extra-precision (XP) docking was employed to identify the compounds with the most favorable XP docking scores. Further analysis using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method to calculate the overall free binding energy. The binding energy between the prospective ligand molecule and the target protein Bcl-2 was assessed by a 100 ns molecular dynamics simulation for curcumin and Epigallocatechin gallate (EGCG). The findings of this investigation demonstrate the identification of a molecular structure that effectively inhibits the functionality of the Bcl-2 when bound to the ligand EGCG. Consequently, this finding presents a novel avenue for the development of pharmaceuticals capable of effectively addressing both inflammatory and tumorous conditions.

Investigation of cholinesterase and α-glucosidase enzyme activities, and molecular docking and dft studies for 1,2-disubstituted cyclopentane derivatives with phenyl and benzyl units.

Six known products (4-9) were prepared from reaction of adipoyl chloride with 1,2,3-trimethoxybenzene according to the literature. From (2,3,4-trimethoxyphenyl)(2-(2,3,4-trimethoxyphenyl)cyclopent-1-en-1-yl)methanone (4) of them, four new 1,2-disubstituted cyclopentane derivatives (10-13) with phenyl and benzyl units were synthesized by reactions such as hydrazonation, catalytic hydrogenation and bromination. The obtained compounds 4-13 were examined for their in vitro inhibitory activity against acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and α-glucosidase enzymes. All compounds 4-13 showed inhibition at nanomolar level with Ki values in the range of 45.53 ± 7.35-631.96 ± 18.88nM for AChE, 84.30 ± 9.92-622.10 ± 35.14nM for BChE, and 25.47 ± 4.46-48.87 ± 7.33 for α-Glu. In silico molecular docking studies of the potent compounds were performed in the active sites of AChE (PDB: 1E66), BChE (PDB: 1P0I), and α-glucosidase (PDB: 5ZCC) to compare the effect of bromine atom on the inhibition mechanism. The optimized molecular structures, HOMO-LUMO energies and molecular electrostatic potential maps for the compounds were calculated by using density functional theory with B3LYP/6-31 + G(d,p).

Asymmetric cobalt porphyrins for pH-universal oxygen reduction reactions: Benzoic acid advances phenyl as substituents

Asymmetric metalloporphyrins are potential electrocatalysts to construct composites for efficient oxygen reduction reactions (ORRs) due to their inherent large dipole moment, which facilitates the charge separation. To find more effective molecular structures towards the ORRs, in particular their performance and electrolyte relationship, we rationally designed two A3B-type asymmetric cobalt porphyrin aPh-TCoP and aBA-TCoP with phenyl and benzoic acid as substituents, respectively. The ORR performance of the porphyrin-decorated carbon black composites was examined in five electrolytes at different pH values spanning from 0.7 to 13.7. It was found that aBA-TCoP/C exhibited better ORR activity and selectivity than aPh-TCoP/C in all solutions. Interestingly, both composites demonstrated their highest ORR activity in the pH13.7 electrolyte and exhibited 4-electron selectivity in the pH3.7 solution. This conclusion is drawn from a comprehensive analysis of various electrochemical properties, encompassing current density, reduction potentials, electron transfer numbers, and intermediate yields. The results illustrate the regulation of ORR properties by altering the electrolyte pH and a notable improvement in the ORR performance through the modification of porphyrin substituents. These findings offer a foundational understanding for the design of efficient metalloporphyrins and the attainment of controlled oxygen reduction in electrochemical devices.

Epigallocatechin gallate and curcumin inhibit Bcl-2: a pharmacophore and docking based approach against cancer

The protein Bcl-2, well-known for its anti-apoptotic properties, has been implicated in cancer pathogenesis. Identifying the primary gene responsible for promoting improved cell survival and development has provided compelling evidence for preventing cellular death in the progression of malignancies. Numerous research studies have provided evidence that the abundance of Bcl-2 is higher in malignant cells, suggesting that suppressing Bcl-2 expression could be a viable therapeutic approach for cancer treatment. In this study, we acquired a compound collection using a database that includes constituents from Traditional Chinese Medicine (TCM). Initially, we established a pharmacophore model and utilized it to search the TCM database for potential compounds. Compounds with a fitness score exceeding 0.75 were selected for further analysis. The Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis identified six compounds with favorable therapeutic characteristics. The compounds that successfully passed the initial screening process based on the pharmacodynamic model were subjected to further evaluation. Extra-precision (XP) docking was employed to identify the compounds with the most favorable XP docking scores. Further analysis using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method to calculate the overall free binding energy. The binding energy between the prospective ligand molecule and the target protein Bcl-2 was assessed by a 100 ns molecular dynamics simulation for curcumin and Epigallocatechin gallate (EGCG). The findings of this investigation demonstrate the identification of a molecular structure that effectively inhibits the functionality of the Bcl-2 when bound to the ligand EGCG. Consequently, this finding presents a novel avenue for the development of pharmaceuticals capable of effectively addressing both inflammatory and tumorous conditions.