Results Of Molecular Dynamics Simulations Research Articles

Identification of the potential TLR7 antagonists by virtual screening and experimental validation.

Toll-like receptor 7 (TLR7) is highly expressed in dendritic cells (DCs) and B cells, and its aberrant activation can promote disease progression in systemic lupus erythematosus (SLE). We utilized structure-based virtual screening and experimental validation to screen natural products from TargetMol for potential TLR7 antagonists. Our results of molecular docking and molecular dynamics simulation showed that Mogroside V (MV) strongly interacted with TLR7, with stable open-TLR7-MV and close-TLR7-MV complexes. Furthermore, in vitro experiments demonstrated that MV significantly inhibited B cell differentiation in a concentration-dependent manner. In addition to TLR7, we also revealed a strong interaction of MV with all TLRs, including TLR4. The above results suggested that MV might be a potential TLR7 antagonist deserving of further study.

Viscosity and structure of CaO–Al2O3–TiO2-based mold fluxes with various CaO/Al2O3 mass ratios

ABSTRACT The effects of CaO/Al2O3 mass ratio on the viscosity and structure of new CaO–Al2O3–TiO2-based fluorine-free mold fluxes for high titanium steel are investigated by viscometer, molecular dynamics (MD) simulations and Raman spectroscopy. When the CaO/Al2O3 mass ratio increased from 0.6 to 1.4, the viscosities and activation energies reduced from 0.43 to 0.10 Pa·s and 127.8–74.2 kJ·mol−1, respectively. While the break temperatures raised from 1385 to 1507 K. Moreover, according to MD simulation results, the concentration of high coordination of Al–O and Ti–O bonds decreased, and the complex structure units of Q3, Q4 and Q5 turned to the simple structure units of Q0, Q1 and Q2. Raman spectra suggested that the concentrations of Ti–O–Ti(Al) linkage and Q2(Si-O−) decreased significantly, but the concentration of Q1(Si–O−) increased. Therefore, CaO/Al2O3 could simplify the network structure and decrease the viscosity of new CaO–Al2O3–TiO2-based fluorine-free mold fluxes for high titanium steel.

Shear behavior of SiCf/SiC interface under the thermo-chemo-mechanical influence and machine-learning-based interfacial microstructure design

The mechanical behavior of composite interface can be influenced by multiple factors, including the morphological roughness, the structure of coating interphase, and the temperature. Here, high-throughput molecular dynamics (MD) simulations are carried out to investigate the entangled effects of these factors on the shear stiffness , the friction coefficient , the debonding strain and stress , of SiCf/SiC interface. We find that is maximized by small roughness and high temperature for the optimal chemical bonding effect; and are maximized by large roughness and low temperature, taking advantage of the mechanical interlocking effect while avoiding cusp softening; demonstrates two local maxima which result from the competition between chemical bonding and mechanical interlocking. Provided the MD simulation results, a variational autoencoder (VAE) model is proposed to design the microstructure of SiCf/SiC interface for desired shear properties. According to the validations, the VAE-predicted interfacial configuration demonstrates highly similar shear properties to the reference one, justifying its potential for the microstructure design of composite interface. The results of this work can be employed to facilitate the development of SiCf/SiC composite by taking advantage of the synergistic effects of multiple designable factors.

In silico molecular study of hepatitis B virus X protein as a therapeutic target

The Hepatitis B virus is a leading cause of liver cirrhosis and hepatocellular carcinoma. HBx viral protein is considered a contributor to pathogenesis and hepatocarcinogenesis. This study aimed to screen the effect of some antiviral compounds to target HBx protein for inhibition of its function. Here, molecular docking, molcular dynsmic simulation, MM/GBSA and T-SNE methods were applied to study the complex stability and to cluster the conformations that generated in the simulation. Among the 179 compounds screened in this study, three antiviral agents (SC75741, Punicalagin, and Ledipasvir) exhibited the lowest docking energy and best interaction. Among these compounds, SC75741 was identified as a potent inhibitor of HBx that showed the best and most stable interaction during molecular dynamic simulation, and blocking a region near to HBx helix resides (aa 88-100) that is associated with cell invasion. The analysis of relative binding free energy through MM/GBSA for molecular dynamic simulation results revealed binding energy −9.9 kcal/mol for SC75741, −11 kcal/mol for Punicalagin, and −10.1 kcal/mol for Ledipasvir. These results elucidate the possible use of these compounds in the research for targeting HBx. Communicated by Ramaswamy H. Sarma

Antibacterial Potential of Trihydroxycyclohexa-2,4-Diene-1-Carboxylic Acid: Insight from DFT, Molecular Docking, and Molecular Dynamic Simulation

In this study, (z)-5-((3-(2,3-dihydroxyphenyl) acryloyl) oxy)- 1,3,4-trihydroxycyclohexa-2,4-diene-1-carboxylic acid (chlorogenic acid) was isolated and characterized using UV-Visible, 1H NMR and 13C NMR, FT-IR, along with detailed investigation using density functional theory (DFT), in-silico molecular docking, and molecular dynamics (MD) simulation. Results from DFT calculation indicates that the titled compound is very stable with energy gap of 3.7–7.8 for variable functionals, and similarly, the structural parameters show very close agreement with X-ray data for bond lengths and angles. The FT-IR spectrum results revealed stretching vibration O–H (3366 cm−1), C=O (1689 cm−1), C–H (1636, 1606, 1522, and 1442 cm−1), C–O (1192 and 1122 cm−1). The drug-likeness analyses and ADME studies showed drug-likeness ability and good oral behavior of the investigated compound as it obeys Lipinski, Ghose, Veber and Egan rules. Hepatotoxic and immunotoxic activities were indicated for the toxicity/toxicological endpoints of the studied compound. The molecular docking indicates a binding affinity of −8.30 and 9.5 kcal/mol for the titled compound, which is higher than the standard drug. From the molecular dynamic simulation results, chlorogenic-2H14 (complex B) revealed variations in RMSD values of less than 3Å, indicating that the protein structure underwent minor conformational changes throughout the simulation. Chlorogenic-protein complexes had average RGyr values of 3.704 − 4.907Å, which indicates compaction during the simulation. Therefore, it can be said that the titled compound has potential to be effective as an agent for cholera management, and the results obtained can be platform further in-vitro, vivo and clinical trials.

Janus-functionalization induced magnetism and improved optoelectronic properties in two-dimension silicene and germanene: insights from first-principles calculations

In this paper, the structural stability, optoelectronic and magnetic properties of silicene and germanene monolayers Janus-functionalized simultaneously with hydrogen and alkali metal atoms (Li and Na) are investigated systematically by using first-principles calculations. The calculated results of the ab initio molecular dynamics simulations and cohesive energies indicate that all functionalized cases have good stability. Meanwhile, the calculated band structures show that all functionalized cases retain the Dirac cone. Particularly, the cases of HSiLi and HGeLi show metallic nature but retain semiconducting characteristics. Besides, the above two cases can present obvious magnetic behavior and their magnetic moments are mainly originated by the p states of Li atom. The metallic property and weak magnetic character can also be found in the case of HGeNa. While the case of HSiNa exhibits the nonmagnetic semiconducting property with a indirect band gap of 0.42 eV calculated by the HSE06 hybrid functional. It is also found that the optical absorption in the visible region of silicene and germanene can be effectively improved by Janus-functionalization. Specifically, a high optical absorption of visible light in an order of 4.5 × 105 cm−1 can be observed in the case of HSiNa. Furthermore, in the visible region, the reflection coefficients of all functionalized cases can also be enhanced. These results demonstrate the feasibility of the Janus-functionalization method to modulate the optoelectronic and magnetic properties of silicene and germanene, expanding their potential applications in the fields of spintronics and optoelectronics.

Revealing the mechanism underlying the effects of γ-aminobutyric acid-dioscorin interactions on dioscorin structure and emulsifying properties by molecular dynamic simulations

Many studies have shown that γ-aminobutyric acid (GABA) exhibits various beneficial biological activities, including gut-modulating, neuro-stimulating, and cardio-protecting activities. Naturally, GABA exists in small amounts in yam, which is primarily synthesized by the decarboxylation of L-glutamic acid in the presence of glutamate decarboxylase. Dioscorin, the major tuber storage protein of yam, has been shown to have good solubility and emulsifying activity. However, how GABA interacts with dioscorin and affects their properties has yet to be clarified. In this research, the physicochemical and emulsifying properties of GABA-fortified dioscorin, which was dried by spray drying and freeze drying, were studied. As results, the freeze-dried (FD) dioscorin produced more stable emulsions, while the spray-dried (SD) dioscorin adsorbed more rapidly to oil/water (O/W) interface. The fluorescence spectroscopy, ultraviolet spectroscopy and circular dichroism spectroscopy showed that GABA changed the structure of dioscorin, by exposing its hydrophobic groups. The addition of GABA significantly promoted the adsorption of dioscorin to the O/W interface and prevented droplets coalescence. The results of molecular dynamics simulation (MD) showed that GABA destroyed the H-bond network between dioscorin and water, increased surface hydrophobicity and finally improved the emulsifying properties of dioscorin.

Combining experiments and molecular dynamics simulations to investigate the effects of water on the structure and mechanical properties of a coal gangue-based geopolymer

The effects of water on the structure and mechanical properties of a coal gangue-based geopolymer were investigated experimentally and compared with the results of molecular dynamics simulations. The chemical composition and crystalline phases of the raw materials were analyzed via X-ray fluorescence and X-ray diffraction (XRD) after 28 days of curing, and the mechanical properties were tested. Molecular structure models for H2O/Al ratios of 2.5, 3, and 3.5 were established using molecular dynamics simulation software, and structural optimization and molecular dynamics simulations were performed under the universal force field. Based on the obtained results, the energy and temperature change curves, simulated XRD spectrum, radial distribution function, hydrogen bonding, mean squared displacement, and mechanical properties of the amorphous geopolymer were analyzed. The rationality of the molecular model was verified through comparison with the results of the molecular dynamics simulations and experiments, and as the H2O/Al ratio increased within a given range, the energy and temperature stability time of the system are decreased, the area of the dispersion peak is decreased, the amorphous phase is increased, the diffusion degree of Si and Al in the system is decreased, the length of Si-O bond, Al-O bond, H-O bond and O-O bond is shortened, and the structure is more stable. The mechanical properties obtained from the experiment were also improved.

Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses

Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy. Communicated by Ramaswamy H. Sarma

Molecular Dynamics Simulation of the Influence of External Electric Fields on the Glass Transition Temperature of the Ionic Liquid 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide

We present the results of molecular dynamics simulations of the ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [C2C1im][NTf2] in the presence of external electric fields (EEFs) of varying strengths to understand the effects of EEFs on the glass transition temperature Tg. We compute Tg with an automated and objective method and observe a depression in Tg when cooling the IL within an EEF above a critical strength. The effect is reversible, and glasses prepared with EEFs recover their original zero-field Tg when heated. By examining the dynamics and structure of the liquid phase, we find that the EEF lowers the activation energy for diffusion, reducing the energetic barrier for movement and consequently Tg. We show that the effect can be leveraged to drive an electrified nonvapor compression refrigeration cycle.

A dual functional polypeptide with antibacterial and anti-inflammatory properties for the treatment of periodontitis

Periodontitis has been reported as the sixth most prevalent disease in human beings. This destructive disease is closely related to systemic diseases. Existing local drug delivery systems for periodontitis suffer from poor antibacterial effect and drug resistance. Inspired by the pathogenesis of periodontitis, we implemented a strategy to construct a dual functional polypeptide LL37-C15, which exhibited remarkable antibacterial effect against P. gingivalis and A. actinomycetemcomitans. In addition, LL37-C15 inhibits the release of pro-inflammatory cytokines by controlling the inflammatory pathway and reversing macrophage M1. Furthermore, the anti-inflammatory effect of LL37-C15 was also verified in vivo in a periodontitis rat model through the morphometry and histological observations of alveolar bone, hematoxylin-eosin, and Trap staining in gingival tissue. The results of molecular dynamics simulations showed that LL37-C15 could selectively destroy the bacterial cell membrane and protect the animal cell membrane in a self-destructive manner. The results showed that the polypeptide LL37-C15, as a novel promising therapeutic agent, exhibited a great potential for the periodontitis management. What's more, this dual functional polypeptide provides a promising strategy for building a multifunctional therapeutic platform against the inflammation and other diseases.

Structure Regulation of Electric Double Layer via Hydrogen Bonding Effect to Realize High‐Stability Lithium‐Metal Batteries

The interfacial chemistry of solid electrolyte interphases (SEI) on lithium (Li) electrode is directly determined by the structural chemistry of the electric double layer (EDL) at the interface. Herein, a strategy for regulating the structural chemistry of EDL via the introduction of intermolecular hydrogen bonds has been proposed (p‐hydroxybenzoic acid (pHA) is selected as proof‐of‐concept). According to the molecular dynamics (MD) simulation and density functional theory (DFT) calculation results, the existence of hydrogen bonds realizes the anion structural rearrangement in the EDL, reduces the lowest unoccupied molecular orbital (LUMO) energy level of anions in the EDL, and the number of free solvent molecules, which promotes the formation of inorganic species‐enriched SEI and eventually achieves the dendrite‐free Li deposition. Based on this strategy, Li||Cu cells can stably run over 185 cycles with an accumulated active Li loss of only 2.27 mAh cm−2, and the long‐term cycle stability of Li||Li cells is increased to 1200 h. In addition, the full cell pairing with the commercial LiFePO4 (LFP) cathodes exhibits stable cycling performance at 1C, with a capacity retention close to 90% after 200 cycles.

Molecular Dynamics Simulation of Shock Wave Propagation in Aluminum Single Crystal

The characteristics of shock wave propagation in aluminum single crystal are simulated by using the molecular dynamics (MD) method based on the embedded atom method (EAM) potential function. The structure of the shock front and the Hugonoit relation are obtained. The simulated results show that a two-wave structure exists in the aluminum single crystal for the particle velocity bellower than 2 km/s and the velocity of the elastic wave increases slightly with the shock loading. While only plastic wave exists in the aluminum single crystal for the particle velocity higher than 2 km/s and the width of the shock front decreases by exponent with the normal stress. The MD simulation results are basically consistent with the experimental results.

Five Bonds to Carbon through Tri-Coordination in 
 Al3C3−/0

Here, five bonds to carbon through tri-coordination are theoretically established in the global minimum energy isomers of Al3C3− anion (1a) and Al3C3 neutral (1n) for the first time. Various isomers of Al3C3−/0 are theoretically identified using density functional theory at the PBE0-D3/def2-TZVP level. Chemical bonding features are thoroughly analyzed for these two isomers (1a and 1n) with different bonding and topological quantum chemical tools, such as adaptive natural density partitioning (AdNDP), Wiberg Bond Indices (WBIs), nucleus-independent chemical shifts (NICS), and atoms in molecules (AIM) analyses. The structure of isomer 1a is planar with C2v symmetry, whereas its neutral counterpart 1n is non-planar with C2 symmetry, in which its terminal aluminum atoms are out of the plane. The central allenic carbon atom of isomers 1a and 1n exhibits tri-coordination and thus makes it a case of five bonds to carbon, which is confirmed through their total bond order as observed in WBI. Both the isomers show σ- and π-aromaticity and are predicted with the NICS and AdNDP analyses. Further, the results of ab initio molecular dynamics simulations reveal their kinetic stability at room temperature; thus, they are experimentally viable systems.

The role of Aedes aegypti in inducing/aggravating IgE-mediated allergic airway disease: extensive computational studies for identification of allergenic proteins

Respiratory allergies have become a major public health concern and affect one-third of the world’s population. Several factors like environmental changes, industrialization, and immunologic interactions are reported to contribute to allergic respiratory diseases. Immunological reactions because of mosquito bite (allergic proteins) have been reported to have a high contribution to IgE-mediated allergic airway disease but they are largely ignored. In this study, we aim to predict the potential allergens (proteins) from Aedes aegypti that might play a role in the reactions of IgE-mediated allergic airway diseases. The allergens are identified from an extensive literature search and the 3D structures were prepared using the SwissDock server. Computational studies were performed to identify the potential allergens that might be responsible for IgE-mediated allergies. Our docking and molecular dynamics (MD) simulation results suggest that ADE-3, an allergen from Aedes aegypti, has the highest docking score and is predicted to be responsible for IgE-mediated allergic reaction(s). Overall, this study highlights the importance of immunoinformatics, and the obtained information can be used for designing prophylactic peptide vaccine candidates and inhibitors for controlling IgE-mediated inflammations. Communicated by Ramaswamy H. Sarma

Trans-scale rough surface contact model based on molecular dynamics method: Simulation, modeling and experimental verification

Contact interfaces widely exist in mechanical structures from macroscopic to microscopic scales and play an important role in understanding the properties and dynamics of the structures. To obtain the contact behavior, it is essential to include the plastic deformation characteristics on rough surfaces (caused by dislocation in asperity), while they are not properly considered in the traditional macroscopic models. This work presents a trans-scale rough surface contact model with the combination of the macroscopic model and the microscopic deformation mechanism by MD simulation. (I) Based on the molecular dynamics (MD) simulation results of a single-asperity normal contact, the relationship between the critical interference and the asperity size is fitted. The results show that the critical interference of the asperity is affected by its size, especially at the microscopic scale. Large asperity produces small critical interference. (II) A trans-scale rough surface contact model was established based on the fitted curves, which considered the joint distribution of asperity radius and height and the asperity size effect. (III) The influence of parameters was analyzed, and the predicted results of the proposed model and the traditional models were compared with the experimental results and MD simulation results. The results show that compared with other traditional models, the proposed trans-scale model has better performance in describing the normal contact characteristics of rough surfaces at both macroscopic and microscopic scales, showing the ability of full-scale description.

Origin of the elastic anisotropy of silica particles: Insights from first-principles calculations and nanoindentation molecular dynamic simulations

To better elucidate and comprehend the origin of the elastic anisotropy observed in silica sand, this study investigates the nanoscale mechanical properties of α-quartz (the main component of silica sand) using the first-principles calculations (density functional theory, DFT) and nanoindentation molecular dynamics (MD) simulations. The cell parameters and elastic constants (Cij) of α-quartz are obtained by DFT with PBESOL functional. The electron density difference of the most commonly exposed crystal surfaces {100}, {001}, and {101}, exhibits significant distinction, which is considered as the underlying cause of α-quartz's elastic anisotropy. This study reveals a significant difference in Young's modulus E, Poisson's ratio v, and hardness H along different directions, which are also visualized in three dimensional graphics. Notably, E{100} = 81.576 GPa < E{001} = 101.198 GPa < E{101} = 113.323 GPa, and H{001} = 9.068 GPa < H{100} = 11.258 GPa < H{101} = 19.870 GPa. The change in E calculated by MD simulations is consistent with DFT calculations. Additionally, this study observed distinct initiation of yielding during nanoindentation for different crystal surfaces, with the corresponding indentation yielding depth following the trend D{100} > D{001} > D{101}. Furthermore, both DFT and MD simulation results indicate that the negative v effect on E is negligible in α-quartz.

Baicalein Inhibits the Staphylococcus aureus Biofilm and the LuxS/AI-2 System in vitro.

Staphylococcus aureus (S. aureus) is a common cause of mastitis in dairy cows, a condition that has a significant economic impact. S. aureus displays quorum sensing (QS) system-controlled virulence characteristics, like biofilm formation, that make therapy challenging. In order to effectively combat S. aureus, one potential technique is to interfere with quorum sensing. This study evaluated the effects of different Baicalin (BAI) concentrations on the growth and the biofilm of S. aureus isolates, including the biofilm formation and mature biofilm clearance. The binding activity of BAI to LuxS was verified by molecular docking and kinetic simulations. The secondary structure of LuxS in the formulations was characterized using fluorescence quenching and Fourier transform infrared (FTIR) spectroscopy. Additionally, using fluorescence quantitative PCR, the impact of BAI on the transcript levels of the luxS and biofilm-related genes was investigated. The impact of BAI on LuxS at the level of protein expression was also confirmed by a Western blotting investigation. According to the docking experiments, they were able to engage with the amino acid residues in LuxS and BAI through hydrogen bonding. The results of molecular dynamics simulations and the binding free energy also confirmed the stability of the complex and supported the experimental results. BAIshowedweak inhibitory activity against S. aureus but significantly reduced biofilm formation and disrupted mature biofilms. BAI also downregulated luxS and biofilm-associated genes' mRNA expression. Successful binding was confirmed using fluorescence quenching and FTIR. We thus report that BAI inhibits the S. aureus LuxS/AI-2 system for the first time, which raises the possibility that BAI could be employed as a possible antimicrobial drug to treat S. aureus strain-caused biofilms.

Diffusion coefficient and the volume swelling of CO2/light oil systems: Insights from dynamic volume analysis and molecular dynamics simulation

The oil volume expansion and CO2 diffusion are one of the main mechanism of CO2-enhanced oil recovery (CO2-EOR). This paper established a series of experiments, numerical simulations, and molecular dynamics (MD) simulations to describe mass transfer behaviors between oil–gas phases. Expressly, the CO2 diffusion coefficient and light oil swelling factor are signification parameters to quantify and analyze these behaviors. In detail, the CO2 diffusion coefficient and the oil swelling factor were obtained from the traditional pressure decay method and the advanced MD simulation. Synthetically, the pressure decay method and MD simulation results were mutually verified. The results showed that the equilibrium pressure was proportional to the mole fraction of CO2 and inversely proportional to the mole fraction of light oil. The equilibrium time was proportional to the mole fraction of CO2 and light oil. At the temperature of 333.15 K and the initial pressure of 7.5 MPa, the CO2 diffusion coefficient in light oil was positively correlated with the relative molar proportion of CO2, while the light oil swelling factor was vice versa. In addition, the closer to the CO2-light oil interface, the greater the light oil's potential energy and self-diffusion coefficient, and the stronger the transport ability.

Comprehensive analysis (aerobic/anaerobic, molecular recognitions, band-position and degradation-mechanism) of undoped and Co-doped anatase-brookite - An experimental/theoretical evaluation of the less-studied TiO2 mixed phase

The molecular recognition (MRec) effect is required in the initial phase of organic reactions. The second stage involves molecular-orientations and molecular-orbitals energy-levels (MOrbE). The components of a reaction must be compatible in terms MRec and MOrbE. Therefore, the comprehension of photocatalytic systems applied in wastewater treatment will be improved if the MRec effect is also considered as an important factor. The purpose of this study is to provide a comprehensive understanding of the less studied anatase-brookite mixed-phase (doped and undoped). Anatase/brookite photocatalytic systems were evaluated utilizing experimental/theoretical approaches in H2O (aerobic/anaerobic) environments with Vis-light and the organic pollutant (OrPo) methyl orange (MO). The compatibility of MRec and MOrbE of anatase-brookite mixed-phase (with the different reactive system components) confirmed this is the optimal combination for photocatalytic application. Using the sol-gel method, AM-TiO2NP (amorphous), TiO2NP (crystalline), and TiO2NP-Co0.1 at% (crystalline Co-doped) anatase-brookite mixed-phase photocatalysts were obtained. The morphology and surface were characterized using XRD, BET, SEM, HR-TEM, FT-IR and XPS. Employing UV–vis DRS and PL, photo-response and electron-hole recombination were studied. LVS and Mott-Schottky plot were employed to determine photo-electrochemical activity. The results of TiO2NP photocatalytic degradation in both aerobic and anaerobic environments are remarkable. The results of molecular dynamics (MD) simulation and Fukui Function (FF) based on density functional theory (DFT) validate the remarkable photocatalytic MO degradation.