MD Results Research Articles

Evolution of microstructure and grain boundaries during annealing of high-purity tantalum materials

The microstructure and texture evolution of tantalum (Ta) during annealing were studied in this work, in addition to simulating and analyzing of the grain boundary motions and their interactions using molecular dynamics simulations (MD). The results showed that the evolution of the recrystallized texture in the surface region of Ta is different from that in the core region. Coincident site lattice (CSL) is significantly related to the grain orientation and thus directly affects the recrystallization texture. MD results showed that the grain boundary mobility rate is higher at low angle grain boundaries (LAGB), which implied that the mobility rate is influenced by the tilt angle. Lower mobility rate of high angle grain boundary (HAGB) possibly caused by a large number of stabilized Σ3 grain boundaries (GBs) between them. It is shown that the inhomogeneous distribution of the recrystallization texture during the annealing process can be possibly attributed to the presence of a large number of Σ3 GBs.

The synergetic effect of He and Kr irradiation on helium bubble evolution in SiC/SiC composite: Combining in-situ TEM observation with MD simulation

SiC fiber reinforced SiC matrix composites (SiC/SiC composites) are considered as one of the promising structural materials for liquid type breeding blanket in the fusion energy system. The transmutation gas production rate in fusion reactor is significantly higher compared with fission reactors. An innovative method combining in-situ irradiation and TEM observation and MD simulation was utilized to evaluate the synergetic effects of helium and irradiation on SiC/SiC composites. A comprehensive experiment matrix including Kr irradiation, He pre-implantation with sequential Kr irradiation as well as simultaneous dual beam at 1073 K to 16 dpa and 2400 appm He (150 appm/dpa) was performed using 800 keV Kr and 50 keV He ions. With the support of MD results, the impact of relative concentration ratio of vacancies and helium atoms on the bubble evolution was systematically investigated and the corresponding mechanism was further unraveled, which provides the basis of limiting the bubble density in SiC/SiC composites. Additionally, the direct evidence for the competition of irradiation-assisted bubble growth and re-dissolution was in-situ observed in SiC matrix for the first time.

COMPARISON OF SITA STANDARD 24-2 WITH SITA FASTER 24-2C PROGRAM ON HUMPHREY FIELD ANALYZER IN ASSESSING VISUAL FIELD DEFECTS OF GLAUCOMA PATIENTS

Introduction & ObjectivesIntroduction: Periodical perimetry examination to detect and determine the rate of glaucomaprogression continues to be a challenging task, because it depends on many factors. Besides, thereis now a paradigm shift which central visual field defects occur earlier. SITA Standard (SS) 24-2 isthe clinical standard for glaucoma examination, but there were studies reporting on the prevalenceof central visual field defects not detected. SITA Faster (SFR) 24-2C was developed to addresscurrent shortcomings, but the performance has yet to be formally and independently assessed.Objectives: To compare the global indices (Mean Deviation, Pattern Standard Deviation, Visual FieldIndex) and test duration between SS 24-2 and SFR 24-2C program.
 MethodsThis is an analytical observational study with a cross-sectional design. Subjects aged >18 years whodiagnosed with glaucoma and whose visual fields unaffected by other condition besides glaucomawere included. All subjects underwent testing of both programs.
 ResultsThis study was conducted in 94 eyes of 66 patients. Comparison of global indices and test durationbetween the two programs was carried out by the Wilcoxon test. The mean results of MD and PSDglobal indices were not significantly different, however there was a difference in the mean VFI of1.5% between the two programs. The test duration of SFR 24-2C was 55.03% faster.
 ConclusionThere was no significant difference in the MD and PSD global indices, but there was a significantdifference in the VFI, as well as the test duration between the two programs.

COMPARISON OF SITA STANDARD 24-2 WITH SITA FASTER 24-2C PROGRAM ON HUMPHREY FIELD ANALYZER IN ASSESSING VISUAL FIELD DEFECTS OF GLAUCOMA PATIENTS

Introduction: Periodical perimetry examination to detect and determine the rate of glaucoma progression continues to be a challenging task, because it depends on many factors. Besides, there is now a paradigm shift which central visual field defects occur earlier. SITA Standard (SS) 24-2 is the clinical standard for glaucoma examination, but there were studies reporting on the prevalence of central visual field defects not detected. SITA Faster (SFR) 24-2C was developed to address current shortcomings, but the performance has yet to be formally and independently assessed. Objective: To compare the global indices (Mean Deviation, Pattern Standard Deviation, Visual Field Index) and test duration between SS 24-2 and SFR 24-2C program. Methods: This is an analytical observational study with a cross-sectional design. Subjects aged >18 years who diagnosed with glaucoma and whose visual fields unaffected by other condition besides glaucoma were included. All subjects underwent testing of both programs. Results: This study was conducted in 94 eyes of 66 patients. Comparison of global indices and test duration between the two programs was carried out by the Wilcoxon test. The mean results of MD and PSD global indices were not significantly different, however there was a difference in the mean VFI of 1.5% between the two programs. The test duration of SFR 24-2C was 55.03% faster. Conclusion: There was no significant difference in the MD and PSD global indices, but there was a significant difference in the VFI, as well as the test duration between the two programs.

DFT and Molecular Dynamics Simulation Studies of 4-(2-(2-(2- Chloroacetamido)phenoxy)acetamido)-3-Nitrobenzoic Acid and 4-(2- (Benzo[D]thiazol-2-ylthio)acetamido)-3-Nitrobenzoic Acid against Escherichia coli ParE Enzyme

Background: The increased emergence of multidrug-resistant bacterial strains is a continuous life-threatening global problem. The best approach to prevent the reproduction and invasion of the pathogenic bacteria is to inhibit the replication stage. The untapped molecular machinery involved in the replication is ParE subunit of topoisomerase IV. In this study, compounds active against the ParE were selected. Objective: This study aimed to analyze the electronic parameters, chemical stability, kinetic stability, and binding modes of the compounds. Methods: Density functional theory (DFT) and molecular electrostatic potential (MESP) calculations were computed using Jaguar with a basis set of 6-31G**++ (B3LYP) in the gas phase. MD simulation was performed for the 100 ns using Desmond available in Maestro to determine the stability and obtain an insight into the molecular mechanism of E. coli ParE docked complexes. Results: From the DFT calculations, the energy gap ΔE -7.58 and -7.75 eV between the HOMO and LUMO of both the compounds P1 (4-(2-(2-(2-chloroacetamido)phenoxy)acetamido)-3-nitrobenzoic acid) and P2 (4-(2-(benzo[d]thiazol-2-ylthio)acetamido)-3-nitrobenzoic acid) explained the chemical and kinetic stability of the system. MD results demonstrated the minimum fluctuations and conformational stability of the protein structures. Conclusion: The P1 and P2 compounds were chemically and kinetically stable. Furthermore, MD results demonstrated the stability and inhibitory action of the ligands dependent on hydrophobic, ionic and water bridges than that of hydrogen-bonding interactions.

Viscosity Reduction Mechanism and Rheological Properties of Ethylene-Bis-Stearamide and Crumb Rubber Modified Asphalt

This study investigates the effect of ethylene-bis-stearamide (EBS) on viscosity reducing of crumb rubber modified asphalt (CRMA) and explores the interaction mechanism via molecular dynamics simulation (MD), microscope method and rheological experiment. It is confirmed that the EBS play an important role in reducing the viscosity of ethylene-bis-stearamide and crumb rubber modified asphalt (EBS-CRMA), especially when the content is within 3%. The micro morphology and MD results showed that the EBS is coating on rubber and asphaltenes and then forming lubrication film, which is the main reason leading to the viscosity decrease of EBS-CRMA. Additionally, other factors also have significant effect in reducing the viscosity of EBS-CRMA, including the more uniform distribution of asphaltenes, the enhanced diffusion ability of saturates and resins, the reduction of hydrogen bonds and soluble substances within asphalt phase. When EBS content exceeds 3%, the influence on viscosity of EBS-CRMA is not obvious with the EBS content continuously increasing. It can be concluded from Fourier Transform Infrared (FTIR) Spectrometer and MD results that the molecular aggregation, the concentration increase of intermolecular hydrogen bonds and the diffusion ability decrease of EBS-CRMA molecular system are main reasons. Meanwhile, the coating effect of EBS and soluble substances concentration within asphalt phase are limited as the EBS content over 3%.

Molecular Docking and Molecular Dynamic Simulation on the Interaction of Saffron’s Active Compunds with HER-2 Protein

Human epidermal growth factor receptor-2 (HER-2) is an essential oncogene in breast cancer. HER-2 causes 25% of breast cancer, and this type of cancer tends to grow and spread faster than others but had a good response to HER-2 targeted therapy. This study aims to analyze chemical compounds in saffron plants (Crocus sativus) that potential to breast anticancer activity by inhibiting HER-2 receptor (PDB ID: 3RCD). The study employed in silico research such as molecular docking using AutoDock Tools software, and visualization with Biovia Discovery Studio. In addition, molecular dynamic simulation was conducted using GROMACS software, with visualization performed using Grace. The molecular docking results showed that Crocetin has a lower binding energy value of -8.37 kcal/mol compared to Herceptin, which is -7.11 kcal/mol and the lowest energy among Saffron bioactive compounds. These results indicated that the affinity of Crocetin in binding to HER-2 receptor is better than Herceptin. The molecular interactions were hydrogen, hydrophobic, electrostatic, and unfavorable bonds. The MD results showed that the RMSD value meets the 0.2-0.5 nm stability requirements. According to the data analysis, Herceptin appears to have a more stable RMSF value when compares to Crocetin. The Rg graph of both complexes showed stability until the end of the simulation. The H-bond results show that the Herceptin complex has more hydrogen bonds than the Crocetin complex. These results showed that the chemical components of saffron plants have the potential as breast anticancers by inhibiting the HER-2 receptor.Keywords: anticancer, Crocus sativus, HER-2 receptor, molecular docking, molecular dynamic.

New insights into the adsorption and assembly of mixed collectors with different carbon chain lengths on the low-rank coal flotation by sum-frequency vibration spectroscopy and molecular dynamics simulation

In low-rank coal (LRC) mixed collectors, little attention has been paid to the structure-activity relationship of different carboxylic acids. In this study, the application effect and adsorption mechanism of the mixed collector composed of dodecane (D) and carboxylic acid with different carbon chain lengths (n-valeric acid (VA), n-decanoic acid (DA), myristic acid (MA)) for LRC were explored by using sum-frequency vibration spectroscopy (SFG) and molecular dynamics simulation (MD). SFG measured the groups orientation angle on the LRC surface treated with the mixed collector, revealing that during the interfacial assembly process of mixed collector molecules, D molecules and the main molecular axes of DA molecules with similar carbon chain length tend to be adsorbed parallel to the LRC surface. The MD results showed that adding D-DA could weaken the hydrogen bonding between the LRC surface and interfacial water to the greatest extent, thereby improving every component's diffusion ability.

Electrical Erosion Resistance of Graphene Reinforced Cu-W Circuit Breaker Contact Materials under 5 kA Arc

This work integrates experimental and MD simulation approaches to study the role of graphene in G-Cu-W composites. Arcing tests were conducted on G-Cu-W and Cu-W contact samples under a 5kA peak current. Experimental results show that adding graphene leads to a lower surface roughness of the sample following arcing. MD simulation results indicate that the G-Cu-W model exhibits a smoother surface and fewer lost metal atoms than the Cu-W model due to the protective effect of graphene layer.

Evaluation of dimedone-derived compounds as inhibitors against human colon cancer: Insights from 2D-QSAR, ADMET prediction, Osiris, Molinspiration, and molecular modeling

For this research, we performed a 2D-QSAR analysis on a set of 34 molecules derived from dimedone with inhibitory activity against human colon cancer (HT-29). The investigation incorporated principal component analysis (PCA), multiple linear regression (MLR), multiple non-linear regression (MNLR), and artificial neural network (ANN). The evaluations of the QSAR models demonstrated high predictive power (R2MLR = 0.884; R2CV (MLR) = 0.86), (R2MNLR = 0.810; R2CV (MNLR) = 0.879), and (R2ANN = 0.9; R2CV (ANN) = 0.89). The reliability of the models was validated through internal, external, Y-randomization, and validation domain applicability assessments. Utilizing the QSAR model predictions, we designed four new molecular structures that exhibited superior inhibitory activity against the HT-29 human colon cancer cell line compared to the 34 previously tested compounds. Subsequently, we examined the ADMET predictions, Molinspiration, and Osiris properties of the four compounds. The results revealed excellent ADMET predictions and Molinspiration for all four compounds, while only one designed compound fulfilled all Osiris properties. Molecular docking was employed to investigate the bindings between the newly designed molecule C and the c-Met protein. The findings indicated that the newly designed compound exhibited high stability in c-Met. Finally, MD simulations were employed to assess the stability and binding modes of compound C. Based on the MD results, compound C shows promise as a potential c-Met agonist candidate. Overall, our results suggest that this investigated compound has the potential to serve as a novel inhibitor against human colon cancer.

The role of hydrophobic interactions in the molten globule state of globular protein modulated by surfactants.

In order to highlight the role of hydrophobic interactions in the molten globule (MG) state of globular protein modulated by surfactants, the interactions of bovine α-lactalbumin (α-LA) with alkyl trimethylammonium bromides (CnTAB, n=10, 12, 14, and 16) have been studied by experimental and theoretical techniques. Isothermal titration calorimetry (ITC) showed that the enthalpy changes (ΔH) and area of the enthalpogram increased with increasing the chain length of CnTAB. The result of fluorescence, circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectrum suggested that C10TAB and C12TAB unfolded α-LA partially, C14TAB reconstructed protein with a native-like secondary structure content, and C16TAB induced an MG state α-LA. The SAXS results confirmed that the tertiary structure of α-LA was disrupted by C16TAB forming an MG state complex with a micelle-like structure even at the surfactants concentrations below CMC. As indicated by MD results, the β-domain and unstructured region(s) were involved in the MG state α-LA modulated by CnTAB. This work not only provides molecular insights into the role of hydrophobic interactions in the MG state of a globular protein but also helps understand the mechanism of preparing α-LA based biomacromolecule modulated by hydrophobic interactions.

Theoretical investigation of protective graphene-coated metakaolin geopolymer interface under moisture and chemical composition effects

Improving the durability of metakaolin aluminosilicate materials (named geopolymer) is a key challenge in the building industry. One approach to enhancing these materials resistance to water infiltration and other aggressive agents is to modify their surface properties. This study investigates the atomic-level interfacial interactions between a nanodroplet of water and a graphene-coated geopolymer surface. Using molecular dynamics and density functional theory methods, we computed the surface adsorption and free energies for metakaolin geopolymer surfaces, varying the chemical composition content between Si and Al atoms. Our MD results demonstrate that graphene-coating increases the geopolymer surface's stability, reducing its surface energy from 151 meV/ Å2 to 7.71 meV/ Å2. Moreover, the graphene-coated surface's contact angle with a water nanodroplet increased remarkedly from 31° to 79°, significantly reducing water permeability. We also found that the mobility of water molecules on the coated surface was twenty times lower, with a diffusion coefficient of 0.131 × 10−10 m2.s−1. Importantly, our study revealed the crucial role of interfacial chemical bonding, with the evaluated elastic and indentation moduli increasing 70 and 39 times, respectively, when the interfacial bonding concentration was 14.15%. Our findings provide fundamental insights into the interactions between graphene-coated geopolymer surfaces and water nanodroplets, representing a crucial step towards the development of superhydrophobic geopolymer materials.

Probing the interaction and aggregation of lysozyme in presence of organophosphate pesticides: a comprehensive spectroscopic, calorimetric, and in-silico investigation

Organophosphorus pesticides (OPs) are widely used in agriculture and may contaminate food or water, leading to potential health risks. However, there are few reports on the effect of OPs on protein conformation and aggregation. Hence, in this paper, we have characterized the impact of two OPs, chlorpyrifos (CPF) and methyl parathion (Para), on the model protein HEWL using biophysical and computational methods. The steady-state and time-resolved spectroscopy, Circular dichroism (CD), molecular dynamics simulation, and isothermal titration calorimetry were employed to investigate the binding interactions between HEWL and OPs. The steady-state and time-resolved fluorescence spectroscopy confirm the presence of both static and dynamic quenching between OPs and proteins. Based on fluorescence, MD, and CD results, it was found that the OPs not only show strong binding but also destabilize the protein structure and alter the secondary and tertiary structure of the protein. The molecular docking results showed that OPs entered the binding pocket of the HEWL molecule and interacted through hydrophobic and hydrogen bond interactions. The thermodynamic studies indicated that the binding was spontaneous and OPs have shown an effect on the aggregation process of HEWL. Finally, the protein aggregation process was studied using fluorescence and SDS-PAGE studies in the presence of both the OPs and found to enhance the aggregation process in the presence of OPs. These results provide insights into the potential health risks associated with OPs and highlight the importance of understanding their interactions with biological macromolecules. Communicated by Ramaswamy H. Sarma

Interactions between humulinone derived from aged hops and protein Z enhance the foamability and foam stability

Foam is one of the important characteristics of beer, including foamability, foam stability and foam texture. Protein Z (PZ) is considered to be an important component of beer foam. In this study, the interaction between PZ and humulinone, a widespread compound in aged hops, and the effect on foam properties of PZ were investigated. The fluorescence spectra showed that the stoichiometric ratio of humulinone to PZ was 4.25 ± 0.48: 1, and the binding constant was (1.64 ± 0.17) × 105 M−1. MD and FTIR results showed that the main force of interaction between PZ and humulinone was hydrogen bond, and the possible sites were Asn-37, Ser-292, Lys-290 and Pro-395. Moreover, the addition of humulinone greatly reduced the surface tension of PZ solution, and changed the secondary structure of PZ, which is beneficial for the foam stability. Under the influence of humulinone, the foamability, foam stability and foam texture of PZ all increased.

Comprehensive insight into the molecular interaction of rutin with human transferrin: Implication of natural compounds in neurodegenerative diseases

Neurodegeneration, a process of irreversible neuronal damage, is characterized by a damaged neuronal structure and function. The interplay between various proteins maintains homeostasis of essential metals in the brain, shielding neurons from degeneration; human transferrin (Htf) is essential in maintaining iron homeostasis. Any disruption in iron homeostasis results in the development of neurodegenerative diseases (NDs) and their pathology, mainly Alzheimer's disease (AD). Rutin is a known compound for its neuroprotective effects. In this work, we deciphered the binding of rutin with Htf in a bid to understand the interaction mechanism. The results of fluorescence and UV–vis spectroscopy demonstrated strong interaction between rutin and Htf. The enthalpy change (∆H°) and entropy change (∆S°) analysis demonstrated hydrophobic interactions as the prevalent forces. The binding mechanism of rutin was further assessed atomistically by molecular docking and extensive 200 ns molecular dynamic simulation (MD) studies; molecular docking showed binding of rutin within Htf's binding pocket. MD results suggested that binding of rutin to Htf does not cause significant structural switching or disruption of the protein's native packing. Overall, the study deciphers the binding of rutin with hTf, delineating the binding mechanism and providing a platform to use rutin in NDs therapeutics.

An experimental and molecular dynamics study on the formation of low-energy grain boundaries induced by grain rotation during rapid solidification

The interaction between the massive δ-Fe nuclei during rapid solidification is studied through atomization and molecular dynamics simulation of Cu-Fe monotectic alloys, based on its liquid separation behavior. The experimental results showed that Σ1/3/9 grain boundaries (GBs) with lower interfacial energy are preferentially expressed. MD results further proved that δ-Fe nuclei in liquid Cu can rotate to Σ1/3 relationship, following the boundary energy reduction path. Therefore, the mechanism of special grain boundary formation through grain rotation in rapid solidification processes is demonstrated.

Computational Prediction of 3,5-Diaryl-1H-Pyrazole and spiropyrazolines derivatives as potential acetylcholinesterase inhibitors for alzheimer disease treatment by 3D-QSAR, molecular docking, molecular dynamics simulation, and ADME-Tox

The efficacy of 40 synthesized variants of 3,5-diaryl-1H-pyrazole and spiropyrazoline’ derivatives as acetylcholinesterase inhibitors is verified using a quantitative three-dimensional structure-activity relationship (3D-QSAR) by comparative molecular field analysis (CoMFA) and molecular similarity index analysis (CoMSIA) models. In this research, different field models proved that CoMSIA/SE model is the best model with high predictive power compared to several models (Qved2 = O.65; R2 = 0.980; R2test = 0.727). Also, contour maps produced by CoMSIA/SE model have been employed to prove the key structural needs of the activity. Consequently, six new compounds have been generated. Among these compounds, M4 and M5 were the most active but remained toxic and had poor absorption capacities. While the M1, M2, M3 and M6 remained highly active while respecting ADMET's characteristics. Molecular docking results showed compound M2 better with acetylcholinesterase than compound 22. The interactions are classical hydrogen bonding with residues TYR:124, TYR:72, and SER:293, which play a critical role in the biological activity as AChE inhibitors. MD results confirmed the docking results and showed that compound M2 had satisfactory stability with (ΔGbinding = −151.225 KJ/mol) in the active site of AChE receptor compared with compound 22 (ΔGbinding = −133.375 KJ/mol). In addition, both compounds had good stability regarding RMSD, Rg, and RMSF. The previous results show that the newly designed compound M2 is more active in the active site of AChE receptor than compound 22. Communicated by Ramaswamy H. Sarma

Effect of intercalated and exfoliated graphite particles on the mechanical properties of polymer composite: A micromechanics-computational approach

This study investigated the effects of intercalation and exfoliation of the graphite flake particles on the mechanical properties of elastomeric composites using analytical, computational, and experimental techniques. Relying on the modified Eshelby and incremental Mori–Tanaka approach, a new micromechanics model was proposed to estimate Young’s modulus and develop a constitutive model for expanded graphite (EG)-filled elastomer in finite strain deformation. It was found that when the initial graphite flakes expanded, the actual volume fraction and ultimate aspect ratio of the dispersed particles significantly affected the mechanical properties of the EG-reinforced composites. The present model and subsequent predictions reflect the initial flake diameter, actual volume fraction, ultimate aspect ratio of the particles, and other convenient physical properties of the composite constituents. In addition, molecular dynamics simulations were performed to evaluate the elastic properties of the EG-Matrix interphase region using the COMPASS force field function. The MD results showed that Young’s modulus of the interphase region increased significantly as the quantity of the graphene layer increased. The micromechanics-constitutive model results were validated using the experimentally determined stress–strain relation of the composites. EG- and CB-elastomer nanocomposite specimens were fabricated and tested in the experimental program. Field emission scanning electron microscopy (FESEM) analysis of the cryo-fractured surfaces of the elastomer compounds showed good interactions between the constituents. Numerical computations indicated that the proposed model incorporating the new parameters could accurately predict the experiment at a small particle concentration.

Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against Cutibacterium acnes sialidase

Cutibacterium acnes is an opportunistic pathogen linked with acne vulgaris, affecting 80–90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in C. acnes virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for C. acnes resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as −10.2, −10.1, −9.9 and −9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (ΔG) −29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors. Communicated by Ramaswamy H. Sarma

Spectroscopic and molecular docking study of three kinds of cinnamic acid interaction with pepsin

In this work, under simulated physiological conditions (pH = 2.2, glycine hydrochloric acid buffer solution), the interactions of cinnamic acid (CA), m-hydroxycinnamic acid (m-CA) and p-hydroxycinnamic acid (p-CA) with pepsin were studied by fluorescence spectroscopy, ultraviolet–visible absorption spectroscopy, circular dichroism (CD) spectroscopy, Fourier transform infrared spectroscopy (FTIR), molecular docking and molecular dynamic simulation (MD). The spectrogram results showed that these three kinds of CA had a strong ability to quench the intrinsic fluorescence of pepsin, and the quenching effects were obvious with the increase of concentration of these three kinds of molecules. The quenching mechanism of CA, m-CA and p-CA on the fluorescence of pepsin was static quenching. In addition, a stable complex was formed between three kinds of CA with pepsin. Thermodynamic data and docking information suggested that three kinds of CA combine with pepsin were mainly driven by electrostatic force and hydrogen bond. The binding constant and the number of binding sites were determined. The interaction of CA, m-CA and p-CA with pepsin was spontaneous, and accompanied by non-radiative energy transfer. The results from CD, FTIR, UV–Vis and synchronous fluorescence spectra measurements manifested that the secondary structure of pepsin was changed by the binding of three kinds of CA. The β-sheet of pepsin increased after the interaction with three kinds of CA. The assay results of pepsin activity showed that three kinds of CA led to a decrease in pepsin activity within the investigated concentrations. Molecular docking investigation revealed the formation of polar hydrogen bonds as well as hydrophobic interactions between three kinds of CA with pepsin, and the ligand within the binding pocket of pepsin. MD results implied the formation of a stable complex between three kinds of CA and pepsin. The research suggested that cinnamic acid and its derivatives could be a potential effect on the structure and properties of digestive enzyme.