Free Energy Of Activation Research Articles

Synthesis, Reaction Mechanism, DNA Cleavage and Antitumor Properties of Naphthoquinone‐Based Enediynes

AbstractUnder physiological conditions, natural enediynes antibiotics generate free radicals through a cycloaromatization reaction. The resulting highly reactive radicals can abstract hydrogen atoms on the phosphate backbone of DNA, leading to high cytotoxicity. On the other hand, anthraquinone‐fused compounds such as daunomycin and adriamycin can insert into DNA through planar aromatic ring structures, resulting in strong DNA damage. To this end, a series of naphthoquinone‐based enediynes were designed and synthesized by adjusting the type of terminal alkyne to modulate their water solubility and radical generation property. Theoretical calculations suggest that the naphthoquinone‐based enediyne generates radicals through a rearrangement (1,3‐proton transfer) followed by Myers‐Saito cyclization processes, with a much lower activation free energy barrier than Bergman cyclization (24.2 kcal/mol vs 39.8 kcal/mol). Differential scanning calorimetry and electron paramagnetic resonance results showed that naphthoquinone‐based enediynes undergo cycloaromatization at relatively low temperatures, resulting in the generation of highly reactive radical species. The enediynes with optimal water solubility displayed strong DNA cleavage ability at micromolar level and high cytotoxicity towards Hela cells, providing a half‐inhibitory concentration of 8.19 μM.

Insights into the physicochemical properties of newly synthesized benzyl triethylammonium chloride-based deep eutectic solvents

In order to utilize deep eutectic solvents (DESs) as a replacement for conventional organic solvents for different applications, a detailed understanding of their physicochemical properties is extremely important. In this study, several novel DESs based on benzyl-triethylammonium chloride (BTEA) as a hydrogen bond acceptor (HBA) and acids/or alcohols as hydrogen bond donors (HBDs) have been synthesized. DESs have been thoroughly characterized and investigated for their physicochemical properties viz. thermal stability, glass transition temperature, viscosity (η), surface tension (γ), refractive index (nD), density (ρ), speed of sound (u), and conductivity (κ) in a temperature range of 293.15–343.15 K. The effect of temperature, type of HBDs, and alkyl chain length of HBDs of the DESs on the physicochemical properties are critically examined and discussed. Viscosity data are fitted to Vogel-Fulcher-Tamman (VFT) and Arrhenius models. A linear model was used to fit surface tension (γ), density, refractive index, and speed of sound data whereas conductivity data were fitted to a nonlinear equation. Primary data on physicochemical properties have been used to estimate the viscous flow parameters (activation entropy, activation enthalpy, and free energy of activation) and other derived parameters such as lattice energy, standard entropy, molar volume, intermolecular free length, and isentropic compressibility. A relationship between molar conductivity and dynamic viscosity has been established to evaluate the ionicity of the synthesized DESs. Insights into the structure–property correlations are discussed in detail.

Transport and optical properties of the binary liquid mixture containing 1,3-diaminopropane and alkyl acetates (C1-C4) at T= (303.15-318.15) K: experimental investigations and theoretical modelling

ABSTRACT Physicochemical properties of pure liquids and their liquid mixtures at different compositions and at different temperatures have a significant role in the optimisation of chemical processes. Present report involves the analysis of the physicochemical properties of 1,3-diaminopropane and alkyl acetate. The viscosity () and refractive index () of 1,3-Diaminopropane, 1,3-DAP (1), with alkyl acetates, AAc, (C1-C4) (2) were measured at different temperatures (T = 303.15 to 318.15 K) under the atmospheric pressure 0.1 MPa. Deviation in viscosity, , deviation in refractive index, , and excess Gibbs free energy of activation, for these binary mixtures were calculated from measured viscosity and refractive index data and fitted to Redlich-Kister polynomial equation (R.K.). The data were analysed in terms of the Graph theoretical approach (GTA) to study the interactions in binary mixtures. The values were also correlated by using Bloomfield and Dewan (BFD) model and various correlations. data were correlated by various relevant correlations.

Controlling Swing Rates in Macrocyclic Molecular Mortise Hinges.

Hinge motion is observed in macrocyclic, mortise-type molecular hinges using variable temperature NMR spectroscopy. The data is consistent with dynamic hinging from a folded-to-extended-to-folded enantiomeric state. Crystallographic and solution structures of the folded states are reported. Chemical shift predictions derived from crystallographic data corroborate fully revolute hinge motion. The rate of hinging is affected by steric congestion at the hinge axis. A macrocycle containing glycine, 1, hinges faster than one comprising aminoisobutyric acid, 2. The free energies of activation, ΔG≠ , for 1 and 2 were determined to be 13.3±0.3 kcal/mol and 16.3±0.3 kcal/mol, respectively. This barrier is largely independent of solvent across those surveyed (CD3 OD, CD3 CN, DMSO-d6 , pyridine-d5 , D2 O). Experiment and computation predict energy barriers that are consistent with disruption of an intramolecular network of hydrogen bonds. DFT calculations reveal a pathway for hinge motion.

Understanding the Fate of the Banert Cascade of Propargylic Azides: Sigmatropic versus Prototropic Pathway.

The Banert cascade is an efficient synthetic strategy for obtaining 4,5-disubstituted 1,2,3-triazoles. The reaction can proceed via a sigmatropic or prototropic mechanism depending on the substrate and the conditions. In this work, the mechanisms of both pathways from propargylic azides with different electronic features were investigated using density functional theory, quantum theory of atoms in molecules, and natural bond orbital approaches. The calculated energy barriers were consistent with the experimental data. Three patterns of electron density distribution on the transition structures were observed, which reflected the behaviors of the reactants in the Banert cascade. The stronger conjugative effects were associated with lower/higher free activation energies of sigmatropic/prototropic reactions, respectively. A clear relationship between the accumulation of the charge at the C3 atom of propargylic azides with the energy barriers for prototropic reactions was found. Thus, the obtained results would allow the prediction of the reaction's course by evaluating reactants.

Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).

Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG‡ ≈ 21 kcal·mol-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF3 or -CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.

Spectroscopic, thermal, and anticancer investigations of new cobalt(II) and nickel(II) triazine complexes

ABSTRACT. The condensation of thiosemicarbazide with oxazolidinone produced 5-benzylidene-3-(4-chloro-phenyl)-6-oxo-5,6-dihydro-1H-[1,2,4]triazine-2-carbothioic acid amide (HL1). Co(II) and Ni(II) ions were reacted with the HL1 ligand. Elemental analysis and molar conductivity, along with mass, 1H-NMR, IR, UV-Vis, and X-ray powder diffraction spectral examinations, were used to reveal the chemical structure of the synthesized complexes. The stoichiometry of the complexes was determined to be 1:2 (metallic: moiety) using analytical, spectroscopic, and thermal data. The thermal properties of the complexes were explored using thermogravimetric (TG-DTG/DTA) methods, as well as the decomposition stages. Several kinetic thermodynamic parameters such as free activation energy (ΔG*), activation enthalpy (ΔH*), activation entropy (ΔS*), pre-exponential factor (A), and the activation energy (E*) were estimated. Inhibitory effects towards colon carcinoma cells (HCT cell line), hepatocellular carcinoma (Hep G2 cell line), and breast carcinoma (MCF-7 cell line) were verified using various concentrations of the samples. A colorimetric method was used to determine the cell viability percent in comparison to doxorubicin drug as a control.
 
 KEY WORDS: 1,2,4-Triazines, Thiosemicarbazide, Thermogravimetric analysis, Non-electrolytes, Anticancer
 Bull. Chem. Soc. Ethiop. 2023, 37(5), 1151-1162. 
 DOI: https://dx.doi.org/10.4314/bcse.v37i5.8

Density functional theory and ab initio molecular dynamics reveal atomistic mechanisms for carbonate clumped isotope reordering.

Carbon (13C) and oxygen (18O) isotopes in carbonates form clumped isotope species inversely correlated with temperature, providing a valuable paleothermometer for sedimentary carbonates and fossils. However, this signal resets ("reorders") with increasing temperature after burial. Research on reordering kinetics has characterized reordering rates and hypothesized the effects of impurities and trapped water, but the atomistic mechanism remains obscure. This work studies carbonate-clumped isotope reordering in calcite via first-principles simulations. We developed an atomistic view of the isotope exchange reaction between carbonate pairs in calcite, discovering a preferred configuration and elucidating how Mg2+ substitution and Ca2+ vacancies lower the free energy of activation (ΔA‡) compared to pristine calcite. Regarding water-assisted isotopic exchange, the H+-O coordination distorts the transition state configuration and reduces ΔA‡. We proposed a water-mediated exchange mechanism showing the lowest ΔA‡ involving a reaction pathway with a hydroxylated four-coordinated carbon atom, confirming that internal water facilitates clumped isotope reordering.

Entropic barrier of water permeation through single-file channels

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. Despite its significance in health and disease as well as for biotechnological applications, the energetics of water permeation are still elusive. Gibbs free energy of activation is composed of an enthalpic and an entropic component. Whereas the enthalpic contribution is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. Here, we estimate, by means of accurate activation energy measurements of water permeation through Aquaporin-1 and by determining the accurate single channel permeability, the entropic barrier of water permeation through a narrow biological channel. Thereby the calculated value for triangle {S}^{{{ddagger}} } = 2.01 ± 0.82 J/(mol·K) links the activation energy of 3.75 ± 0.16 kcal/mol with its efficient water conduction rate of ~1010 water molecules/second. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.

Volumetric and viscometric properties of aqueous 1,2-dimethylethylenediamine solution for carbon capture application

The present work investigates the volumetric and viscometric properties of an aqueous solution of 1,2-dimethylethylenediamine (DEEDA) over an entire concentration range and an absorber operating temperature range of 313.15K–333.15K at atmospheric pressure. The investigated volumetric properties included the density, excess molar volume, partial molar volume, and the investigated viscometric properties included the viscosity, viscosity deviation, free energy for activation of viscous flow, excess free energy for activation of viscous flow, and excess entropy for activation of viscous flow. The results indicated that there are strong intermolecular interactions and suitable molecular packing in the binary DEEDA–water mixture. Hence, the mixture was found to deviate from a real mixture according to the calculated excess properties. The DEEDA solvent's preliminary volumetric and viscometric properties revealed convincing potential as a novel amine for carbon capture. Additionally, the Redlich-Kister-based correlations showed favorable correlative performance for excess molar volume, viscosity deviation, and excess entropy for activation of viscous flow.

Thermo physical properties of diacetone alcohol with isomer butanols at different temperatures and correlation with the Jouyban–Acree model

ABSTRACT Excess molar volume, excess isentropic compressibility, deviation in viscosity and excess Gibbs free energy for activation of viscous flow for binary mixtures of 4-hydroxy-4-methyl-2-pentanone e (DAA) with 1-butanol (B1), 2-butanol(B2) and 2-methyl-2-propanol(B3) components selected compositions were determined from the measured values of densities (ρ), viscosities (), and speeds of sound (u) of pure components and their mixtures at from 303.15 K to 313.15 K. The results are analysed in terms of intermolecular interactions or hydrogen bonding or hetero-association interactions in the binary mixtures. Prigogine-Flory-Patterson (PFP) theory is applied to identify the predominant molecular interaction. Jouyban-Acree model results are discussed in terms of mean relative deviation (MRDs) and individual relative deviation (IRD) between calculated and experimental densities, speeds of sound and viscosities as an accuracy criterion

Solvent Mediated Interactions on Alkene Epoxidations in Ti-MFI: Effects of Solvent Identity and Silanol Density

Selective alkene oxidation rates within zeolite pores reflect differences in contributions from thermodynamic nonidealities introduced by noncovalent interactions at solid–liquid interfaces and spatial constraints enforced by the zeolite topology. Epoxidation turnover rates for 1-hexene in Ti-MFI zeolite differ by 1000-fold across 10 combinations of solvents, including alcohols and acetonitrile, over Ti-MFI with distinct silanol defect densities. Solvent mediated noncovalent interactions persist across an extended binding environment that influences the stability of epoxidation transition states. Apparent activation enthalpies (ΔHApp⧧) and entropies (ΔSApp⧧) span 80 kJ mol–1 and 200 J mol–1 K–1, respectively, with the most positive values for both appearing in methanol. Hydrophilic (i.e., (SiOH)x defect rich) Ti-MFI-OH catalysts in methanol give the greatest turnover rates because entropic gains associated with the disruption of hydrogen-bonded networks of intrapore methanol and water dominate activation free energies. In situ infrared spectra show that the adsorption of 1,2-epoxyhexane to Ti sites disturbs the equilibrium solvent structure within pores in ways that reflect the density of the hydrogen bond donor and acceptors near active sites. This interpretation agrees with measured enthalpies for adsorption of 1,2-epoxyhexane to Ti active sites within solvent filled pores that correlate with ΔHApp⧧ across solvent and catalyst combinations. The displacement of solvent molecules and the associated rupture and formation of hydrogen bonds among solvents, pore walls, and nearby reactive molecules during catalysis and adsorption events incur substantial excess contributions that govern the reaction rates and barriers. These realizations explain the particular success of alkene epoxidations in mixtures of H2O2 and methanol over hydrophilic forms of Ti-MFI in industrial processes (e.g., the hydrogen peroxide–propylene oxide process). These findings demonstrate the gains achieved by appropriately pairing organic solvents with microporous catalysts to manipulate the intrinsic kinetics of reactions and the thermodynamics of adsorption at solid–liquid interfaces.

A Kinetic Model for Describing the Heterogeneity of Susceptibility to Chemical or Physical Change

Molecules in foods and food ingredients exist in a variety of states, each of which has a different susceptibility to chemical and physical change. A model was proposed for the change in behavior over time based on the assumption that the free energy of activation in relation to the rate constant obeyed a Gaussian distribution. This model could well explain the unique behaviors observed in the thermal inactivation of immobilized enzymes, formation of aldehydes from lignin by alkaline nitrobenzene oxidation, autoxidation processes of microencapsulated lipids, flavor release from microcapsules, and desorption of proteinaceous deposits fouled on stainless steel surfaces.

Understanding the atmospheric transformation mechanism of an emerging fluorinated alcohol (FESOH)

One important pathway for human exposure to per- and polyfluorinated alkyl substances (PFASs) is based on the Earth's atmosphere. Figuring out atmospheric transformation mechanism of PFASs is beneficial for understanding their effects on humans. However, the focus on the molecular-level transformation mechanism of emerging PFASs in the atmosphere still need to be improved. In this work, we used quantum chemistry calculation to study ·OH-initiated degradation mechanism of a new fluorinated alcohol (C3F7OCHFCF2SCH2CH2OH, abbreviated FESOH) in the presence of oxygen and nitric oxide. Three main conformers of FESOH share the similar initial mechanism that the abstraction reactions of H atom at α-C and β-C atoms are the main pathways (activation free energies of <10 kcal mol−1 at 298 K), but make different contributions to the whole FESOH degradation. Subsequent transformations starting from initial products at α-C atoms will reunite with that at β-C atoms, and the intermediate (C3F7OCHFCF2S·) is produced. After O2 addition to the intermediate and the following SO2 elimination, the alkyl radical (C3F7OCHFCF2·) can undergo consecutive chain cleavage cycles to form CF3OH finally. The bioaccumulation evaluation shows that FESOH and its transformation products cannot be accumulated in organisms. The work is helpful for knowing the atmospheric fate of FESOH at molecular level and can provide some insight into the transformation of other PFASs in the atmosphere.

Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations.

Combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the catalytic mechanism of human T-cell leukemia virus type 1 (HTLV-1) protease, a retroviral aspartic protease that is a potential therapeutic target for curing HTLV-1-associated diseases. To elucidate the proteolytic cleavage mechanism, we determined the two-dimensional free energy surfaces of the HTLV-1 protease-catalyzed reactions through various possible pathways. The free energy simulations suggest that the catalytic reactions of the HTLV-1 protease occur in the following sequential steps: (1) a proton is transferred from the lytic water to Asp32', followed by the nucleophilic addition of the resulting hydroxyl to the carbonyl carbon of the scissile bond, forming a tetrahedral oxyanion intermediate, and (2) a proton is transferred from Asp32 to the peptide nitrogen of the scissile bond, leading to the spontaneous breakage of the scissile bond. The rate-limiting step of this catalytic process is the proton transfer from Asp32 to the peptide nitrogen of the scissile bond, with a free energy of activation of 21.1 kcal/mol. This free energy barrier is close to the experimentally determined free energy of activation (16.3 kcal/mol) calculated from the measured catalytic rate constant (kcat). This mechanistic study provides detailed dynamic and structural information that will facilitate the design of mechanism-based inhibitors for the treatment of HTLV-1-associated diseases.

Viscosity, Free Activation Energy, and Glass Transition Temperature of Potassium Boron K2O–B2O3 Melts

Viscosity, Free Activation Energy, and Glass Transition Temperature of Potassium Boron K2O–B2O3 Melts

Theoretical insights into the methane catalytic decomposition on graphene nanoribbons edges.

Catalytic methane decomposition (CMD) is receiving much attention as a promising application for hydrogen production. Due to the high energy required for breaking the C-H bonds of methane, the choice of catalyst is crucial to the viability of this process. However, atomistic insights for the CMD mechanism on carbon-based materials are still limited. Here, we investigate the viability of CMD under reaction conditions on the zigzag (12-ZGNR) and armchair (AGRN) edges of graphene nanoribbons employing dispersion-corrected density functional theory (DFT). First, we investigated the desorption of H and H2 at 1200K on the passivated 12-ZGNR and 12-AGNR edges. The diffusion of hydrogen atom on the passivated edges is the rate determinant step for the most favourable H2 desorption pathway, with a activation free energy of 4.17eV and 3.45eV on 12-ZGNR and 12-AGNR, respectively. The most favourable H2 desorption occurs on the 12-AGNR edges with a free energy barrier of 1.56eV, reflecting the availability of bare carbon active sites on the catalytic application. The direct dissociative chemisorption of CH4 is the preferred pathway on the non-passivated 12-ZGNR edges, with an activation free energy of 0.56eV. We also present the reaction steps for the complete catalytic dehydrogenation of methane on 12-ZGNR and 12-AGNR edges, proposing a mechanism in which the solid carbon formed on the edges act as new active sites. The active sites on the 12-AGNR edges show more propensity to be regenerated due lower free energy barrier of 2.71eV for the H2 desorption from the newly grown active site. Comparison is made between the results obtained here and experimental and computational data available in the literature. We provide fundamental insights for the engineering of carbon-based catalysts for the CMD, showing that the bare carbon edges of graphene nanoribbons have performance comparable to commonly used metallic and bi-metallic catalysts for methane decomposition.

Theoretical study to gain fundamental insight into reaction mechanism of N-S acyl transfer of N-sulfanylethylanilide-based protein labeling reagent on protein surface.

Elucidation of protein function is one of the central issues in the field of life sciences. To study the function of proteins not in isolation, but in a cell or its lysate, thus, it is necessary to selectively label the target protein in a mixture. Affinity labeling is one of several widely used methods for selective labeling; however, this method has the disadvantage that the labeling reagent is always activated, albeit weakly. Therefore, fine-tuning of the reactivity and/or reaction conditions is generally required for successful target-selective labeling. We previously developed a new affinity labeling reagent with N-sulfanylethylanilide (SEAlide) as a key reactive unit. It was designed based on the following hypotheses. SEAlide is less reactive and does not label in the absence of a target protein. Upon target binding, amino acid side-chain functional groups on the target surface convert SEAlide into a thioester form via N-S acyl transfer, allowing the target to be labeled. However, no evidence has been obtained so far to directly prove the hypothesis. In this study, we examine whether amino acid side-chain functional groups can activate SEAlide from the viewpoint of theoretical chemistry. The theoretical studies show that the activation free energy and enthalpy of the acyl transfer of SEAlide are reduced in the presence of methylammonium, which is a model for the protonated side chain of Lys, and acetate, which is a model for the deprotonated side chain of Asp/Glu. It suggests that Lys and Asp/Glu side chains could potentially stabilize the activation transition states to accelerate the thioester formation. Furthermore, the significant decrease in the activation enthalpy indicates that the contribution of entropy to the transition state is large. This result supports the original hypothesis that the SEAlide-based labeling reagent is efficiently activated by binding to the target protein.

Selenite-Decorated Polycrystalline NiO Nanosheets Generated from Cathodic Reconstruction for Electrocatalytic Hydrogen Production.

Precatalyst reconstruction in alkaline hydrogen evolution reaction (HER) usually leads to changes in the morphology, composition, and structure, thus improving the catalytic activity, which recently receives intensive attention. However, the design strategies of cathodic reconstruction and the structural features of reconstruction products have not achieved a profound understanding. Here, from the point of thermodynamic stability, metastable nickel selenite dihydrate (NiSeO3·2H2O) is deliberately fabricated as a precatalyst to comprehensively study the reconstruction dynamics in alkaline HER. Multiple in/ex situ techniques capture the geometric, component, and phase evolutions, proving that NiSeO3·2H2O can be transformed into SeO32--decorated polycrystalline NiO nanosheets with rich active sites and good conductivity under alkaline HER conditions, which act as a real catalytic active species. Density functional theory calculations demonstrate that the adsorption of SeO32- can further promote the HER activity of NiO due to the optimized free energy of water activation and hydrogen adsorption. As a result, the SeO32--NiO catalyst exhibits a low overpotential at -10 mA cm-2 (90 mV) and long-term stability (>100 h). This work highlights the targeted design of precatalyst to trigger and utilize cathodic reconstruction and provides an available method for the development of adsorption-modulated efficient electrocatalysts.

Anticorrosive properties of aqueous Cichorium intybus seeds extract as a sustainable-green inhibitor for aluminum corrosion in hydrochloric acid solution: An experimental and DFT/MC/MD theoretical approach

The inhibitory effect of Cichorium intybus seeds (C. Intybus) on the corrosion behavior of Al 7075 alloy was evaluated in a 1 M HCl acid solution using chemical and electrochemical methods. The adsorption process was proved using FTIR, UV-Vis, Fluorescence, SEM, EDX, AFM, and contact angle measurements. The results reflect that C. Intybus provided excellent protection, and all measurements showed that the inhibition performance of extracts increased by increasing the concentration to reach 93.67% at 12% v/v. Furthermore, this substance functioned as a mixed-type inhibitor to obstruct the anodic and cathodic active sites on the surface of the metal. The study outcomes matched the monolayer Langmuir isotherm, and the calculated adsorption free energy and activation energy reflect that the inhibition mechanism featured the physisorption process. The computational studies were used to provide further confirmation of the adsorption mechanism and to find out how organic inhibitor molecules interact with metal surface using Density Functional Theory (DFT) with Lee/Yang/Parr (B3LYP) level, 6–311 + + G(d,p) as the basis function set calculation, Monte Carlo (MC), and Molecular Dynamic (MD) simulations. The findings showed good agreement with both the experimental and theoretical results. One of the important findings of this work is the possibility of using C. Intybus as a greener alternative and environmentally friendly resource for corrosion inhibition in an acidic medium.