1,976 results on '"md"'
Search Results
2. Probing the mechanism of antioxidant and oxidative stability properties of gallic acid and its esters in natural esters: Computational investigations and experiments
- Author
-
Zhang, Kai, Huang, Zhengyong, and Li, Jian
- Published
- 2025
- Full Text
- View/download PDF
Catalog
3. Study on damage defects of Cr coating on Zr alloy surface irradiated by high-dose Au2+: HRTEM observation and molecular dynamics simulation
- Author
-
Yan, An, Luan, Baifeng, Zhou, Hongling, Liu, Congqing, Chen, Lijun, Yang, Xiaoling, Zhu, Xiaoyong, Zhang, Fuen, Xu, Chunrong, Sun, Chao, Ruan, Haibo, and Huang, Weijiu
- Published
- 2025
- Full Text
- View/download PDF
4. Design, synthesis, molecular docking, dynamics simulations and antiviral activities of quinoline derivatives
- Author
-
Singh, Vishal K., Rai, Shivangi, Parihar, Apoorva Singh, Ahmad, Iqrar, Patel, Harun, Schols, Dominique, and Singh, Ramendra K.
- Published
- 2025
- Full Text
- View/download PDF
5. Structural and spectroscopic study of L-tryptophan dimer state using DFT and MD: Computational and experimental analysis
- Author
-
Hssain, Ala Hamd, Gomti Devi, Th., Salih, Rangeen Othman, and Abdullah, Nzar Rauf
- Published
- 2025
- Full Text
- View/download PDF
6. A dynamic coupling scheme for fluid system by combining lattice Boltzmann method and molecular dynamics.
- Author
-
Wang, Yuqing and Zhou, Wenning
- Subjects
- *
COUPLING schemes , *LATTICE Boltzmann methods , *POISEUILLE flow , *FLUID dynamics , *COUETTE flow - Abstract
The coupling of numerical methods in different scales is of great significance in the investigation of intricate multiscale phenomena. This work develops a dynamic coupling approach based on domain decomposition by combining the mesoscale lattice Boltzmann method (LBM) and microscale molecular dynamics (MD) simulations. In the proposed scheme, a two-way concurrent exchange of information between different scales has been achieved. At the atomistic scale, the fluid dynamics are modeled through the particle-based MD method on the framework of the open large-scale atomic/molecular massively parallel simulator (LAMMPS). While at the coarse scale, the fluid system is simulated utilizing the LBM approach, which relies on the collision and streaming of the particles constrained in discretized lattices, adhering to the conservation laws of mass and momentum. The exchange of velocity distributions between the two scales was handled. The accuracy and efficiency of the proposed coupling scheme were validated through simulations of the classic Poiseuille and Couette flows. The obtained results show that satisfactory agreement against pure MD results has been achieved. Moreover, a notable improved efficiency as high as 92.8% has been observed for the coupling scheme in comparison to MD simulations. Due to the inherent parallelism of LBM and MD, the proposed coupling scheme exhibits great potential for extended application in studying complex multiscale phenomena with dynamic coupling between different scales. [ABSTRACT FROM AUTHOR] more...
- Published
- 2025
- Full Text
- View/download PDF
7. DFT investigations on the influence of stacking on the electronic structure, absorption, and non-linear optical properties of 3,5-bis[4-(4-methylphenylcarbonyloxy)phenyl]-1,2,4-oxadiazole.
- Author
-
Fazl-Ur-Rahman, Kashifa, Shanker, Govindaswamy, and Periyasamy, Ganga
- Subjects
- *
PHYSICAL & theoretical chemistry , *OPTICAL materials , *OPTICAL devices , *OPTICAL properties , *CIRCULAR dichroism , *OPTOELECTRONIC devices - Abstract
Context: 1,2,4-Oxadiazole serves as a fundamental building block driving advancements across diverse scientific and technological arenas, contributing to the creation of innovative materials for various applications including devices, sensors, medications, agrochemicals, and biomedical instruments. Employing density functional theory (DFT) methods, we investigate the impact of different conformers of an oxadiazole substituted derivative, specifically 3,5-bis[4-(4-methylphenylcarbonyloxy)phenyl]-1,2,4-oxadiazole, in both monomeric and stacked configurations (dimeric and tetrameric). We analyze the electronic structures of various conformers, including assessment of HOMO–LUMO energy gaps, to detect the influence of diverse substituents and stacking arrangements. We have also explored the stability of stacked structure in explicit solvent environment. Additionally, we examine absorption spectra, non-linear optical properties, and electronic circular dichroism to evaluate the potential applications of these molecules in optoelectronic devices. Our calculations showed that all the conformers were thermodynamically stable within an energy difference of 2.64 kcal mol−1. The study also suggests possible application of the material in optical and electronic devices. Methods: DFT calculations were carried out using the CAM-B3LYP and wB97XD functionals with a 6–31 + G* all-electron basis set, paired with the SCRF/PCM solvation model, implemented in the Gaussian 09 package. Equilibrium structure was achieved by performing NPT and NVT simulations using the Gromacs package. [ABSTRACT FROM AUTHOR] more...
- Published
- 2025
- Full Text
- View/download PDF
8. Synthesis, Characterization, Molecular Modeling Studies and Bioactivity of a Novel Bicyclic Compound of δ-lactam with Oxazepine Ring Containing Sulphur Substitute using an Economic Method.
- Author
-
Muslim, Rasim Farraj, Guma, Manaf A., Razzak Mahmood, Ammar A., Ahmad, Iqrar, Hirad, Abdurahman Hajinur, and Patel, Harun
- Subjects
- *
MOLECULAR docking , *BACTERIAL proteins , *SCHIFF bases , *BICYCLIC compounds , *MOLECULAR dynamics - Abstract
Penicillin resistance is a commonly present and controversial matter due to the misuse by people for various reasons. However, few studies have examined the bioactivity of 5- and 6- membered rings. In this study, we aimed to synthesize a new compound containing a 5-membered ring following a short and low-cost method and combined it with oxazepine ring via Schiff bases to produce a bicyclic molecule (Lactozepine).
In vitro examinations were conducted to assess the bioactivity of the prepared compound, including anti-bacterial, anti-fungal and antioxidant activities, which showed a wide zone of inhibition of lactozepine againstStreptococcus pneumoniae but no inhibition was shown againstKlebsiella pneumoniae andStaphylococcus aureus except at a high concentration similar to the result of the anti-fungal assessment. Furthermore, lactozepine showed significant antioxidant activity against free radical formation. The molecular modeling and docking assessment showed the ability of lactozepine to bind to bacterial proteins and inhibit their growth with the lowest free energy for the greatest and strongest binding affinity with the PDB crystal structures 1VQQ, 2WAE, 1PYY and 1IYS ranging from −6.5 and −7.9 kcal/mol. Moreover, the molecular dynamics (MD) simulation showed that RMSF for the assessed protein’s amino acids remained consistent and tightly bound to lactozepine in the dynamic state. The novel compound lactozepine, with δ-lactam rings attached to oxazepine showed bioactivity promising forin vivo studies in the future. [ABSTRACT FROM AUTHOR] more...- Published
- 2024
- Full Text
- View/download PDF
9. High Performance Liquid Chromatography-Tandem Mass Spectrometric determination of carcinogen nitrosamine impurities from pharmaceuticals and DNA binding confirmation aided by molecular docking application.
- Author
-
Daniş, İbrahim, Agar, Soykan, Yurtsever, Mine, and Ünal, Durişehvar Özer
- Subjects
- *
MOLECULAR dynamics , *MOLECULAR docking , *SMALL molecules , *NITROSOAMINES , *NITROSO compounds - Abstract
Background and Aims: Nitrosamines are amine compounds attached to a nitroso group. The reaction of amines and nitrosating agents forms nitrosamines. Nitrosamine impurities are classified as Class 1 based on the carcinogenicity and mutagenicity data by ICH M7 (R1). The recent discovery of nitrosamines in some pharmaceutical products has caused concern. Nitrosamines are carcinogenic, so it is necessary to determine the possible nitrosamines in pharmaceutical products. Methods: An Inertsil ODS-3, (4.6x250 mm, 5 μm) column was used for separation. A triple quadrupole mass detector with electrospray Ionisation (ESI) was used for detection. Multiple reaction monitoring (MRM) was used for quantification. The transition ions are 75.1 > 43.3 for NDMA and 103.0 > 75.1 for NDEA. The calibration curves consist of 5 concentration levels, including NDMA and NDEA (5, 10, 50, 100, 150 ng/mL). The mean r² value was 0.997 for NDMA and 0.999 for NDEA. For NDMA and NDEA, LOD: 2 ng/mL, LOQ: 5 ng/mL. Results: Comprehensive in silico and in vitro results indicate that the method has good accuracy and precision. Conclusion: DNA binding interactions of the molecules NDMA and NDEA, were investigated through the molecular docking and molecular dynamics methods. Molecular Docking simulations showed that these small organic molecules have high-affinity scores and strongly bind to the minor groove of the hDNA via strong hydrogen bonds. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
10. Simulation of Solvatochromic Phenomena in Xanthione Using Explicit Solvent Methods.
- Author
-
Manian, Anjay, Chen, Zifei, Hudson, Rohan J., and Russo, Salvy P.
- Subjects
- *
SOLVENT analysis , *POLYCYCLIC aromatic hydrocarbons , *MOLECULAR dynamics , *SOLVATION , *SOLVENTS - Abstract
Xanthione is a sulfated polycyclic aromatic hydrocarbon which exhibits unique anti-Kasha properties and substantial sensitivity to its medium. Due to this sensitivity however, this makes xanthione-based systems very difficult to simulate. Further, xanthione's is understood to be come more photostable in the presence of a highly polar medium, however whether these photophysical properties could be taken advantage of for certain applications remains to be seen. In clarifying long-held beliefs of specific solvent effects, we apply a rigorous theoretical solvent analysis in both implicit and explicit solvent mediums to elucidate a more complete description of solvent polarity sensitivity in xanthione using both quantum chemical and molecular dynamics techniques. Not only was it found that explicit solvation methods are vital in an accurate description of the system, only a handful of explicit solvent molecules in the simulation are required to yield an appropriate electronic description. This short work is vital to devising future applications for xanthione-based and other quantum technologies, and is an important foundation stone on this journey. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
11. Enhancing oil production via radical reactions during hydrothermal coliquefaction of biomass model compounds and plastics: A molecular dynamic simulation study.
- Author
-
Yan, Shuo, Xia, Dehong, Zhang, Tongtong, and Liu, Xiangjun
- Subjects
- *
MOLECULAR dynamics , *PLASTIC scrap , *SUPERCRITICAL water , *MOLECULES , *RADICALS (Chemistry) - Abstract
[Display omitted] • Radical reactions between biomass and plastic enhance oil production in HTL. • ▪OH radical from oxygenated biomolecule facilitate plastic polymer depolymerizing. • C 1 –C 4 radicals emitted from biomass and plastic polymer recombine as oil molecules. • Lipid and protein could lower the HTL temperatures for plastic polymers. • Feedstock blended ratio plays a crucial role in the reactions during coliquefaction. Recently, hydrothermal coliquefaction of biomass and plastic waste has attracted considerable research interest. However, there is a notable gap in understanding the fundamental reaction mechanisms between biomass and plastics during coliquefaction. This study focused on the coliquefaction of biomass model compounds and plastic polymers using ReaxFF molecular dynamics simulations under both subcritical and supercritical water conditions. Molecular-level tracking and probing of the reaction mechanisms between biomass model compounds and plastics were conducted to purposefully enhance oil production. The study observed related radical reactions between by-product molecules, with detailed mechanisms primarily involving (1) ▪OH radicals released by aqueous phase molecules from biomolecules, transferring as H 2 O molecules and facilitating plastic depolymerization, and (2) C 1 –C 4 radicals in the gaseous phase, emitted from biomolecule and plastic, colliding and subsequently recombining to form oil molecules. Moreover, the yield of multiple products from various mixtures were evaluated by considering the key reaction parameters including reaction temperature and feedstock blended ratio. An exploration into the effect of coliquefaction on oil yield was conducted to precisely identify the optimal coliquefaction conditions. The positive effect of coliquefaction was more pronounced between biomass model compounds and aromatic polymers compared to aliphatic polymers. Analysis of reaction mechanisms and product outcomes has shown that hydrothermal coliquefaction is a viable approach to improving oil production from multi-source organic solid waste. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
12. Quantum Mechanics/Molecular Mechanics Simulations for Chiral-Selective Aminoacylation: Unraveling the Nature of Life.
- Author
-
Ando, Tadashi and Tamura, Koji
- Subjects
ENERGY levels (Quantum mechanics) ,CHEMICAL reactions ,PHENOMENOLOGICAL biology ,BIOLOGICAL systems ,QUANTUM mechanics ,TRANSFER RNA - Abstract
Biological phenomena are chemical reactions, which are inherently non-stopping or "flowing" in nature. Molecular dynamics (MD) is used to analyze the dynamics and energetics of interacting atoms, but it cannot handle chemical reactions involving bond formation and breaking. Quantum mechanics/molecular mechanics (QM/MM) umbrella sampling MD simulations gives us a significant clue about transition states of chemical reactions and their energy levels, which are the pivotal points in understanding the nature of life. To demonstrate the importance of this method, we present here the results of our application of it to the elucidation of the mechanism of chiral-selective aminoacylation of an RNA minihelix considered to be a primitive form of tRNA. The QM/MM MD simulation, for the first time, elucidated the "flowing" atomistic mechanisms of the reaction and indicated that the L-Ala moiety stabilizes the transition state more than D-Ala, resulting in L-Ala preference in the aminoacylation reaction in the RNA. The QM/MM method not only provides important clues to the elucidation of the origin of homochirality of biological systems, but also is expected to become an important tool that will play a critical role in the analysis of biomolecular reactions, combined with the development of artificial intelligence. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
13. Experimental Analysis and Hybrid-Optimization of Micro-ECDM Process Parameters to Enhance Micro-Machining Performances of Silica by Gaussian-Quantum-PSO.
- Author
-
Mondal, Krishnendu, Mallick, Bijan, Hameed, Azzam Sabah, Sarkar, Anindya, Mahato, Jayanta, Dutta, Pijush, and Bose, Bidesh
- Subjects
PARTICLE swarm optimization ,MICROMACHINING ,SURFACE roughness ,MACHINING ,SILICA - Abstract
Nowadays, hybridization of different algorithms for the optimization of non-conventional machining processes tries to accomplish better results. The paper consists of experimental evolutionary-particle Swarm Optimization (PSO), Quantum-PSO and Gaussian Quantum Particle Swarm Optimization (G-QPSO)-based ANN modeling and comparative investigation on performances such as material removal rate (MRR), machining depth (MD), roughness of surface and overcut (OC) for machining of silica by ECDM process using mixed electrolyte. The paper also shows the co-efficient of NN models for different machining criteria and G-QPSO and also the comparative study of MD, roughness (SR), overcut (OC) as well as MRR using different algorithms and convergence test for fitness of experimental results also propounded to achieve cross-validation of models and multi-response optimal results for micro-machining of Silica by ECDM using PSO, QPSO and GQPSO. It is found that Gaussian Quantum Particle Swarm Optimization (G-QPSO)-ANN is more efficient for ECDM and achieves optimal results at 55-volt, pulse on time 52.3 s, inter-electrode gap (IEG) 30 mm, duty ratio 0.475 and electrolytic concentration 30 (wt.%). [ABSTRACT FROM AUTHOR] more...
- Published
- 2025
- Full Text
- View/download PDF
14. Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data
- Author
-
L. América Chi, Jonathan E. Barnes, Jagdish Suresh Patel, and F. Marty Ytreberg
- Subjects
SARS-CoV-2 ,Escape mutation ,DMS ,Antibody ,MD ,FoldX ,Medicine ,Science - Abstract
Abstract Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that higher precision can be achieved using affinity cutoffs tailored to distinct SARS-CoV-2 antibodies from four different classes rather than a one-size-fits-all approach. Further, we suggest that the quartile values of optimized cutoffs reported for each class in this study can serve as a valuable guide for future work on escape mutation predictions. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities. more...
- Published
- 2024
- Full Text
- View/download PDF
15. Comprehensive Analysis of the Effect of New Efficient and High Temperature Resistant Imidazoline Derivatives on the Corrosion Inhibition Performance of Q235: Experimental and Theoretical Studies.
- Author
-
Wang, Pengjie, Fan, Lin, Song, Yuhao, Li, Hao, Ansari, Kashif Rahmani, Li, Zhonghui, Singh, Ambrish, Lin, Yuanhua, and Talha, Mhod
- Subjects
- *
PHOTOELECTRON spectroscopy , *SCANNING electron microscopes , *METAL coating , *DENSITY functional theory , *LANGMUIR isotherms , *CORROSION & anti-corrosives - Abstract
ABSTRACT Background: Imidazoline derivatives were widely used in the field of metal corrosion protection due to the low toxicity and excellent corrosion inhibition performance. In order to further reduce synthesis costs and improve corrosion inhibition performance, oleic acid, diethylenetriamine, and anisaldehyde were used as raw materials to synthesize imidazole Schiff corrosion inhibitors (HM), and the corrosion inhibition mechanism on Q235 in 1.0 mol/L HCl solution was studied rigorously. Method: The corrosion inhibition ability was verified using weight loss and electrochemical experiments. Scanning electron microscope (SEM), energy dispersive spectrometer (EDS), and X‐ray photoelectron spectroscopy (XPS) were used to detect and analyze the protective film formed on the surface of Q235 after weight loss. Density functional theory (DFT) demonstrated the adsorption sites and reaction activity of the corrosion inhibitor, Molecular Dynamics (MD) further validated the corrosion inhibition mechanism. Significant Findings: Imidazoline corrosion inhibitor could form a stable protective film on the surface of Q235. With the concentration increased of HM, the corrosion inhibition efficiency increased gradually, and with the temperature increased, the corrosion inhibition efficiency decreased gradually. At the optimal concentration, the corrosion inhibition rate could reach 98.98%. HM belonged to a mixed type corrosion inhibitor that mainly suppresses the cathode and could spontaneously adsorb on the metal surface, following the Langmuir isotherm for adsorption. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
16. Modelling of SARS-CoV-2 spike protein structures at varying pH values.
- Author
-
Niu, Ziyuan, Kementzidis, Georgios, Zhang, Peng, Zhang, Ziji, Essuman, Bernard, Hasegawa, Karin, Rafailovich, Miriam, Simon, Marcia, Aktas, Bertal Huseyin, Papadopoulos, Evangelos, and Deng, Yuefan
- Subjects
- *
SARS-CoV-2 , *VITRONECTIN , *VIRAL proteins , *PROTEIN structure , *MOLECULAR dynamics - Abstract
Recognising the fact that the SARS-CoV-2 spike glycoprotein is the most crucial protein for the virus's attachment to surfaces and subsequent infection, we carried out massive all-atom molecular dynamics studies of the conformational states of S-protein in solvents of various pH values, ranging from pH = 1 through pH = 11. Our studies found that: (1) The S-protein's structural deviation measured in the backbone at pH = 1 is 185% higher than that of pH = 7, and most of this overall deviation occurs at the receptor-binding domain and N-terminal domain. (2) Structural changes are also observed at both pH = 3 and pH = 11, albeit to a lesser extent than at pH = 1. (3) Changes, as measured by various metrics at pH = 5, pH = 7 and pH = 9, are insignificant. Such a high degree of structural tolerance of the S-protein at these pH values corroborates indirectly with in vitro observations that the virus retains significant infectivity over a wide range of pH. The multiscale structural analyses pinpoint the critical regions that are responsible for the S-protein's structural deviations. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
17. Water desalination, and energy consumption applications of 2D nano materials: hexagonal boron nitride, graphenes, and quantum dots.
- Author
-
Khan, Shahab, Rahman, Faizan Ur, Ullah, Inam, Khan, Salman, Gul, Zarif, Sadiq, Fazal, Ahmad, Tufail, Shakil Hussain, Sayed M., Ali, Ijaz, and Israr, Muhammad
- Subjects
- *
WATER purification , *WATER shortages , *MEMBRANE distillation , *BORON nitride , *QUANTUM dots , *SALINE water conversion - Abstract
In this article, we explore the role of nanotechnology in addressing water scarcity through water desalination. The scope of nanotechnology in water treatment is discussed, emphasizing the potential of 2D nanomaterials such as hexagonal boron nitride (h-BN), graphene, and quantum dots in revolutionizing desalination technologies. Various water desalination techniques, including membrane distillation (MD), solar-powered multi-stage flash distillation (MSF), and multi-effect distillation (MED), are analyzed in the context of nanomaterial applications. The review highlights the energy-intensive nature of conventional water treatment methods and underscores nanomaterials' potential to enhance efficiency and sustainability in water desalination processes. Challenges facing desalination, such as scalability and environmental impact, are acknowledged, setting the stage for future research directions. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
18. Computational Multiscale Study of the Interaction Between the PDMS Polymer and Sunscreen-Related Pollutant Molecules.
- Author
-
Armaković, Stevan, Vujić, Đorđe, and Brkić, Boris
- Subjects
- *
MOLECULAR dynamics , *DENSITY functional theory , *POLAR molecules , *ULTRAVIOLET radiation , *MOLECULAR interactions - Abstract
Sunscreen molecules play a critical role in protecting skin from ultraviolet radiation, yet their efficient detection and separation pose challenges in environmental and analytical contexts. In this work, we employ a multilevel modeling approach to investigate the molecular interactions between representative sunscreen molecules and the polydimethylsiloxane (PDMS) polymer, a material widely recognized for its sorbent properties. Our goal is to explore how these interactions can be fine-tuned to facilitate the effective separation of sunscreen molecules in portable membrane inlet mass spectrometry (MIMS) systems, potentially leading to the development of new membrane materials. Using a combination of advanced computational techniques—force field molecular dynamics simulations, semiempirical GFN2-xTB, and density functional theory calculations—we assess the interaction strength and noncovalent interactions of sunscreen molecules, namely oxybenzone, naphthalene, benzo[a]anthracene, avobenzone, and 1,3,5-trichlorobenzene, with PDMS. Additionally, the effect of temperature on the interaction dynamics is evaluated, with the aim of extending the sorbent capacities of PDMS beyond light polar molecules to larger, polar sunscreen compounds. This study provides critical insights into the molecular-level interactions that may guide the design of novel membrane materials for efficient molecular separation. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
19. Surface Plasmon Resonance Allows to Correlate Molecular Properties With Diffusion Coefficients of Linear Chain Alcohols.
- Author
-
Basile, Giuseppe Stefano, Calcagno, Damiano, Pandino, Irene, Pietropaolo, Adriana, Schifino, Gioacchino, Tuccitto, Nunzio, Zingale, Gabriele Antonio, and Grasso, Giuseppe
- Subjects
- *
SURFACE plasmon resonance , *MOLECULAR dynamics , *INTERMOLECULAR forces , *MOLECULAR shapes , *DIFFUSION coefficients - Abstract
Every biological and physicochemical process occurring in a fluid phase depends on the diffusion coefficient (D) of the species in solution. In the present work, a model to describe and fit the behaviour of D ${D}$ as a function of structure and extensive thermodynamics parameters in binary solutions of linear chain organic molecules is developed. Supporting experimental and computational evidences for this model are obtained by measuring D ${D}$ for a series of n ${n}$ ‐alcohols through a novel surface plasmon resonance method and molecular dynamics simulations. This allows to propose a kind of combined analysis to explain the dependence of D ${D}$ on various thermodynamic and structural parameters. The results suggest that for small linear systems in the range from 0 to 200 g mol−1 and under the assumption that the diffusive activation energy is a linear function of mass, D ${D}$ is strictly dependent on the molecular shape and on the relative strength of the solute‐solvent intermolecular forces represented by a parameter named R. The newly proposed approach can be utilized to characterize and monitor progressive changes in physicochemical properties for any investigated species upon increasing the dimension of the aggregate/molecule along a certain direction. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
20. Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data.
- Author
-
Chi, L. América, Barnes, Jonathan E., Patel, Jagdish Suresh, and Ytreberg, F. Marty
- Subjects
VACCINE effectiveness ,SARS-CoV-2 ,COMPUTER simulation ,REFERENCE values ,IMMUNOGLOBULINS - Abstract
Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that higher precision can be achieved using affinity cutoffs tailored to distinct SARS-CoV-2 antibodies from four different classes rather than a one-size-fits-all approach. Further, we suggest that the quartile values of optimized cutoffs reported for each class in this study can serve as a valuable guide for future work on escape mutation predictions. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
21. Molecular Dynamics Insights into Mechanical Stability, Elastic Properties, and Fracture Behavior of PHOTH-Graphene.
- Author
-
Peng, Qing, Chen, Gen, Huang, Zeyu, Chen, Xue, Li, Ao, Cai, Xintian, Zhang, Yuqiang, Chen, Xiao-Jia, and Hu, Zhongwei
- Subjects
- *
ELASTICITY , *YOUNG'S modulus , *CARBON-based materials , *HYDROGEN atom , *POINT defects - Abstract
PHOTH-graphene is a newly predicted 2D carbon material with a low-energy structure. However, its mechanical stability and fracture properties are still elusive. The mechanical stability, elastic, and fracture properties of PHOTH-graphene were investigated using classical molecular dynamics (MD) simulations equipped with REBO potential in this study. The influence of orientation and temperature on mechanical properties was evaluated. Specifically, the Young's modulus, toughness, and ultimate stress and strain varied by −26.14%, 36.46%, 29.04%, and 25.12%, respectively, when comparing the armchair direction to the zigzag direction. The percentage reduction in ultimate stress, ultimate strain, and toughness of the material in both directions after a temperature increase of 1000 K (from 200 K to 1200 K) ranged from 56.69% to 91.80%, and the Young's modulus was reduced by 13.63% and 7.25% in both directions, respectively, with Young's modulus showing lower sensitivity. Defects usually weaken the material's strength, but adding random point defects in the range of 3% to 5% significantly increases the ultimate strain of the material. Furthermore, hydrogen atom adsorption induces crack expansion to occur earlier, and the crack tip without hydrogen atom adsorption just began to expand when the strain was 0.135, while the crack tip with hydrogen atom adsorption had already undergone significant expansion. This study provides a reference for the possible future practical application of PHOTH-graphene in terms of mechanical properties and fracture failure. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
22. Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies.
- Author
-
Gómez, Sara, Lafiosca, Piero, and Giovannini, Tommaso
- Subjects
- *
PROTOGENIC solvents , *ABSORPTION spectra , *HYDROGEN bonding interactions , *MOLECULAR dynamics , *POLAR solvents - Abstract
We present a comprehensive computational study of UV/Vis absorption spectra of significant food colorants, specifically anthocyanins and curcumin tautomers, dissolved in polar protic solvents, namely water and ethanol. The absorption spectra are simulated using two fully polarizable quantum mechanical (QM)/molecular mechanics (MM) models based on the fluctuating charge (FQ) and fluctuating charge and dipoles (FQF μ) force fields. To accurately capture the dynamical aspects of the solvation phenomenon, atomistic approaches are combined with configurational sampling obtained through classical molecular dynamics (MD) simulations. The calculated QM/FQ and QM/FQF μ spectra are then compared with experiments. Our findings demonstrate that a precise reproduction of the UV/Vis spectra of the studied pigments can be achieved by adequately accounting for configurational sampling, polarization effects, and hydrogen bonding interactions. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
23. Silane-Modified MXene Nanosheets for Improved Anticorrosive Properties of Epoxy Coatings: A Combined Experimental and Computational Study.
- Author
-
Song, Chengjun, Chao, Min, Li, Le, Luo, Chunjia, Chen, Xi, and Yan, Luke
- Abstract
Ti
3 C2 Tx (MXene) nanosheets have been widely noticed and investigated by researchers as a strategy to enhance the anticorrosive properties of epoxy resin (EP) coatings, but their proclivity to accumulate and poor compatibility with the resin matrix limit their further application. In this paper, MXene was modified using a simple one-pot synthesis with (3-glycidoxypropyl)-trimethoxysilane as a surface modifier, and EP composite anticorrosive coatings were prepared using MXene and modified MXene (M-MX) as fillers. Compared with MXene, M-MX has better dispersion in the coating, which can effectively enhance the anticorrosive property of the coating. Among all of the coatings, the composite coating containing 1 wt % M-MX showed the best anticorrosive effect after immersion in a 3.5 wt % NaCl solution for 21 days. The results of salt spray testing and corrosion product analysis indicated that the trend of the corrosion resistance of different coatings was EP < 0.5M-MX < 1MX < 2M-MX < 1M-MX. According to the results of density functional theory and molecular dynamics calculations, all nanosheets were able to block the corrosive medium in the epoxy coatings. Also, M-MX dispersed more uniformly in the composite coatings, which made the system more compact, prolonged the penetration paths of the corrosive medium, slowed down the diffusion of the corrosive medium, and thus provided the coatings with more excellent corrosion resistance properties. [ABSTRACT FROM AUTHOR] more...- Published
- 2024
- Full Text
- View/download PDF
24. Integrating atomistics and experiments in gaining deeper insights into fatigue crack propagation in silver.
- Author
-
Xie, Yinan, Hao, Xiaoli, Wang, Zumin, and Huang, Yuan
- Subjects
- *
CRACK propagation (Fracture mechanics) , *DISTRIBUTION (Probability theory) , *CRYSTAL models , *TRANSMISSION electron microscopy , *FATIGUE testing machines - Abstract
This research utilizes both single crystal and polycrystalline models to probe the fatigue crack propagation mechanism in pure silver via molecular dynamics (MD) simulations. A comprehensive validation approach at both micro and macro scales, incorporating transmission electron microscopy (TEM), electron backscatter diffraction (EBSD), and compact tension (CT) specimen fatigue testing, is developed to verify the reliability of simulation models and results. Simulation findings indicate that the initial crack orientation significantly influences crack propagation. As the crack advances within the crystal, two primary crack propagation mechanisms are discerned: (1) nano-voids appear at the crack tip, and the crack propagates by continuously aggregating with the nano-voids ahead; (2) the formation of Stair-rod dislocations and V-shape stacking faults due to dislocation reactions and slip band movements impedes crack propagation, accompanied by the dislocation reaction of Shockley partial dislocations ( 1 6 <112>) generating Hirth dislocations ( 1 6 <110>). The dislocation reaction is verified through the dislocation analysis of the crack tip area of the CT specimen after fatigue experiment by using TEM. In addition, the results of this study show that the angle between the direction of crack propagation and the grain boundary affects the fatigue crack propagation, e.g. when the angle is less than 60°, the crack rapidly propagates along the grain boundary. The orientation distribution function (ODF) results of EBSD can verify that the polycrystalline model containing 30 grains is a reliable model for the MD simulation of behavior of the crack tip of CT specimen. Lastly, the Paris law constants for pure silver are determined as m = 3.72 and lg C = − 10.77, providing a reference for the fatigue analysis and life prediction of silver components or silver soldering pots in engineering applications. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
25. The Role of Fe(III) in Selective Adsorption of Pullulan on Calcite Surfaces: Experimental Investigation and Molecular Dynamics Simulation.
- Author
-
Ding, Kaiwei, Qiu, Tingsheng, Qiu, Xianhui, Zhao, Guanfei, Jiao, Qinghao, Fang, Jiangjie, Lai, Ruisen, and Yang, Wenhui
- Subjects
- *
POLYSACCHARIDES , *ZETA potential , *CALCITE , *ADSORPTION capacity , *FLUORITE - Abstract
The floatability of fluorite and calcite exhibit similar properties, rendering their flotation separation challenging. Macromolecular polysaccharide reagents containing the polyhydroxyl group have shown broad promising application. The selectivity of polysaccharide is relatively low. In this study, the introduction of Fe3+ was employed to enhance the selective adsorption capacity of Pullulan polysaccharide towards fluorite and calcite minerals, thereby achieving effective flotation separation. Furthermore, the mechanism underlying intramolecular interactions was elucidated. The DFT calculation and XPS analysis revealed that the adsorption of Fe3+ on the calcite surface was more favorable, leading to the formation of a Ca-O-Fe structure. The MD simulation, XPS analysis, and Zeta potential analysis revealed that the Fe-OH groups on the surface of calcite reacted with the -OH groups in Pullulan and formed bonds, resulting in the formation of a Calcite-Fe-Pullulan structure. This facilitated the attachment of a significant number of Pullulan molecules to the calcite surface. The formation of a hydrophilic layer on the outer surface of calcite by Pullulan, in contrast to the absence of such layer on fluorite's surface, results in an increased disparity in surface floatability between these two minerals, thereby enhancing the efficiency of flotation separation. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
26. 無焼成セラミックスのプロセス設計に関わるシミュレーション技術.
- Author
-
石井 健斗, 佐藤 知広, and 藤 正督
- Subjects
SOLIDIFICATION ,SINTERING - Abstract
A non-firing solidification method using surface-activated ceramic powders with mechanochemical treatment and solidified without a high-temperature sintering process has been studied in our group. In this method, the surfaces of ceramic particles are activated by grinding, and this activated state is used as a driving force to bond the particles together. It is essential to computationally understand the mechanical activation and solidification processes in the non-firing process at various molecular and bulk scales. This paper first outlines the differences between the non-firing solidification process and the conventional sintering process. Next, we introduce our simulation results of the non-firing solidification process and discuss future prospects. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
27. Cheminformatics-driven prediction of BACE-1 inhibitors: Affinity and molecular mechanism exploration
- Author
-
Rahul D. Jawarkar, Anam Khan, Suraj N. Mali, Prashant K. Deshmukh, Rahul G. Ingle, Sami A Al-Hussain, Aamal A. Al-Mutairi, and Magdi E.A. Zaki
- Subjects
Alzheimer disease (AD) ,BACE-1 ,QSAR ,Molecular docking ,MD ,MMGBSA ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
The β-secretase, sometimes referred to as BACE1 or Asp2, is the enzyme responsible for initiating the production of Aβ by breaking down the amyloid precursor protein. Hence, BACE is a pivotal target for pharmacological intervention aimed at diminishing the production of Aβ in Alzheimer's disease (AD). We did a quantitative structure-activity relationship (QSAR) study on 1235 compounds that had been experimentally reported as BACE-1 inhibitors (Ki) to find the target molecule and structural patterns linked to blocking the BACE-1 receptor. The OECD-recommended genetic algorithm-multiple linear regression (GA-MLR) QSAR model strikes a good balance between being able to make accurate predictions and understanding how things work. It achieves high values for many evaluation metrics, including R2tr = 0.8047, Q2LMO = 0.802, R2ex = 0.805, CCCex = 0.891, Q2-F1=0.801, Q2-F2=0.799, and Q2-F3=0.815. The mechanistic interpretation of QSAR has identified some nitrogen atoms that are required to block beta-secretase and make it less effective at doing its job. A positively charged aromatic carbon atom has a more significant impact on beta-secretase-1 inhibition. The docking study showed that the catalytic dye residues Asp32 and Asp228 become protonated when compound 27 is present, but they stay unprotonated when compound 27 is not present. These rings of pyrazine and pyridine interact hydrophobically with Tyr71 and Ile118 residues, confirming the pharmacophoric features seen in the QSAR data. We examined the stability of both the protein-ligand complex and the apo-protein. The apoprotein had an average gyration radius of 22.13, whereas the protein-ligand complex had an average gyration radius of 22.91. No changes were made to the results from the molecular docking, molecular dynamics (MD) simulation, MMGBSA (Molecular Mechanics Generalized Born Surface Area), or DFT analyses. Therefore, the current work could effectively contribute to the future development of BACE inhibitors in medication design. more...
- Published
- 2024
- Full Text
- View/download PDF
28. Evaluation of Taraxacum officinale phytoconstituents as potential JNK1 inhibitors: Perspectives from ADMET, molecular docking, molecular dynamics, and density functional theory
- Author
-
Sphelele C. Sosibo, Hendrik G. Kruger, Wonder P. Nxumalo, and Zimbili Zondi
- Subjects
Taraxacum officinale ,c-Jun N-terminal kinase ,Type-2 diabetes ,DFT ,MD ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
The impact of activated c-Jun N-terminal kinase isoform JNK1 chemical pathways in insulin biosynthesis poses a potential health risk of glucose intolerance. Blocking the activity of JNK1 is a promising route for the design of anti-diabetic drugs and associated metabolic syndromes. In this study, 17 extracts of Taraxacum officinale were chosen to bind JNK1 and ascertain their modulatory activity. We employed molecular dynamics, density functional theory and three docking approaches: standard precision, extra precision and quantum polarized ligand docking. The best binding free energy results were obtained from the quantum polarized ligand docking, with myricetin (1) showing a docking score of -10.464 kcal/mol, while quercetin (2) and daphnetin (3) displayed values of -9.769 and -7.136 kcal/mol respectively. Following this, 100 ns molecular dynamics simulations with Desmond showed stabilization average root mean square deviations of 2.34, 2.87, and 2.88 Å for myricetin, quercetin and daphnetin. Further, molecular dynamics revealed complexes of myricetin (ΔG = -38.81 kcal/mol) and quercetin (ΔG = -34.99 kcal/mol) as the most stable inside the JNK1 interface. The energy gaps for myricetin, quercetin and daphnetin were estimated to be 6.17, 6.00 and 6.53 eV employing the M06–2X functional in PCM solvation. Further, myricetin showed the strongest intramolecular hydrogen bonding with -13.06 kcal/mol. This study provides insights into possible anti-type-2 diabetes properties of Taraxacum officinale targeting JNK1. more...
- Published
- 2024
- Full Text
- View/download PDF
29. Numerical Simulation of the Performance of Multistage Direct Contact Membrane Distillation
- Author
-
Al-Muallem, Hussain, Ben-Mansour, Rached, and Antar, Mohammed
- Published
- 2024
- Full Text
- View/download PDF
30. Role of diffusion tensor imaging of extra ocular muscles and orbital fat in Graves’s ophthalmopathy and relation to disease activity
- Author
-
Manar Mansour Hussein, Mohamed Ghonem Mohamed, Amany Abdel Hamid Mousa, Azza Abd El Baky Baiomy, Ahmed Abd El Khalek Abdel Razek, and Mohamed Roshdi Abd El Ghani
- Subjects
DTI ,FA ,MD ,EOMs ,Graves’s ophthalmopathy ,Disease activity ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Abstract Background Graves’ ophthalmopathy (GO) is one of the most common autoimmune inflammatory disorders affecting the orbit that characterized by swelling of extra ocular muscles (EOMs) and expansion of the orbital fat. Diffusion tensor imaging (DTI) could assess the microstructural integrity of tissue. We aimed at this study to assess the role of DTI in the evaluation of EOMs and orbital fat in GO and identify the relationship with disease activity. Results Case–control study included 40 patients diagnosed as Graves’ disease (20 active and 20 inactive) and 10 health control subjects underwent DTI. Low fraction anisotropy (FA) and high mean diffusivity (MD) of inferior rectus (IR), medial rectus (MR) and orbital fat in GO versus healthy control (HC), while high FA and high MD in active group versus inactive group. In order to differentiate between GO and HC; FA cutoff point of IR, MR& orbital fat were 0.46, 0.45 and 0.26 with sensitivity 98.8%,98.8% and 93.8% and specificity 95.0%, 95.0% and 85%, respectively. MD cutoff point for IR, MR and orbital fat 1.24, 1.27 and 1.275 with sensitivity 97.5%, 98.8% and 98.8% and specificity 95.0%, 95% and 95%, respectively. To differentiate between active and inactive GO; FA cutoff point of IR, MR and orbital fat were 0.35, 0.36 and 0.22 respectively with sensitivity 80.0%, 82.5% and 72.5% and specificity 95.0%, 85.0% and 65.0%, respectively. MD cutoff point for IR, MR and orbital fat were 1.58, 1.63 and 1.54 respectively with sensitivity 90.0%, 97.5% and 85.0%, and specificity 90.0%, 80.0% and 62.5%, respectively. Conclusions DTI parameters (FA and MD) of EOMs and orbital fat are considered as crucial radiological biomarkers for diagnosis of GO and could quantitatively differentiate active form inactive disease. more...
- Published
- 2024
- Full Text
- View/download PDF
31. Computational toolbox for the analysis of protein–glycan interactions
- Author
-
Ferran Nieto-Fabregat, Maria Pia Lenza, Angela Marseglia, Cristina Di Carluccio, Antonio Molinaro, Alba Silipo, and Roberta Marchetti
- Subjects
computational tools ,glycan–protein interactions ,md ,molecular recognition ,Science ,Organic chemistry ,QD241-441 - Abstract
Protein–glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein–glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein–ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein–glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions. more...
- Published
- 2024
- Full Text
- View/download PDF
32. 6-Bromo quinazoline derivatives as cytotoxic agents: design, synthesis, molecular docking and MD simulation
- Author
-
Leila Emami, Maryam Hassani, Pegah Mardaneh, Fateme Zare, Maryam saeedi, Mina Emami, Soghra Khabnadideh, and Sara Sadeghian
- Subjects
Cancer ,Quinazoline-4(3H)-one ,MTT ,Docking ,MD ,DFT ,Chemistry ,QD1-999 - Abstract
Abstract Based on unselectively, several side effects and drug resistance of available anticancer agents, the development and research for novel anticancer agents is necessary. In this study, a new series of quinazoline-4(3H)-one derivatives having a thiol group at position 2 of the quinazoline ring (8a-8 h) were designed and synthesized as potential anticancer agents. The Chemical structures of all compounds were characterized by 1H-NMR, 13C-NMR, and Mass spectroscopy. The antiproliferative activity of all derivatives were determined against two cancer cell lines (MCF-7 and SW480) and one normal cell lines (MRC-5) by the MTT method. Cisplatin, Erlotinib and Doxorubicin were used as positive controls. The results of in vitro screening showed that 8a with an aliphatic linker to SH group was the most potent compound with IC50 values of 15.85 ± 3.32 and 17.85 ± 0.92 µM against MCF-7 and SW480 cell lines, respectively. 8a indicated significantly better potency compared to Erlotinib in the MCF-7 cell line. The cytotoxic results obtained from testing compound 8a on the normal cell line, revealing an IC50 value of 84.20 ± 1.72 µM, provide compelling evidence of its selectivity in distinguishing between tumorigenic and non-tumorigenic cell lines. Structure–activity relationship indicated that the variation in the anticancer activities of quinazoline-4(3H)-one derivatives was affected by different substitutions on the SH position. Molecular docking and MD simulation were carried out for consideration of the binding affinity of compounds against EGFR and EGFR-mutated. The binding energy of compounds 8a and 8c were calculated at -6.7 and − 5.3 kcal.mol− 1, respectively. Compounds 8a and 8c were found to establish hydrogen bonds and some other important interactions with key residue. The DFT analysis was also performed at the B3LYP/6–31 + G(d, p) level for compounds 8a, 8c and Erlotinib. Compound 8a was thermodynamically more stable than 8c. Also, the calculated theoretical and experimental data for the IR spectrum were in agreement. The obtained results delineated that the 8a can be considered an appropriate pharmacophore to develop as an anti-proliferative agent. more...
- Published
- 2024
- Full Text
- View/download PDF
33. In silico insights into the design of novel NR2B-selective NMDA receptor antagonists: QSAR modeling, ADME-toxicity predictions, molecular docking, and molecular dynamics investigations
- Author
-
Mohamed El fadili, Mohammed Er-rajy, Somdutt Mujwar, Abduljelil Ajala, Rachid Bouzammit, Mohammed Kara, Hatem A. Abuelizz, Sara Er-rahmani, and Menana Elhallaoui
- Subjects
NMDA receptor ,Analgesic activity ,Molecular modeling ,Neuropathic pain ,MD ,Chemistry ,QD1-999 - Abstract
Abstract Based on a structural family of thirty-two NR2B-selective N-Methyl-D-Aspartate receptor (NMDAR) antagonists, two phenylpiperazine derivatives labeled C37 and C39 were conceived thanks to molecular modeling techniques, as novel NMDAR inhibitors exhibiting the highest analgesic activities (of pIC50 order) against neuropathic pain, with excellent ADME-toxicity profiles, and good levels of molecular stability towards the targeted protein of NMDA receptor. Initially, the quantitative structure-activity relationships (QSARs) models were developed using multiple linear regression (MLR), partial least square regression (PLSR), multiple non-linear regression (MNLR), and artificial neural network (ANN) techniques, revealing that analgesic activity was strongly correlated with dipole moment, octanol/water partition coefficient, Oxygen mass percentage, electronegativity, and energy of the lowest unoccupied molecular orbital, whose the correlation coefficients of generated models were: 0.860, 0.758, 0.885 and 0.977, respectively. The predictive capacity of each model was evaluated by an external validation with correlation coefficients of 0.703, 0.851, 0.778, and 0.981 respectively, followed by a cross-validation technique with the leave-one-out procedure (CVLOO) with Q2 cv of 0.785, more than Y-randomization test, and applicability domain (AD), in addition to Fisher’s and Student’s statistical tests. Thereafter, ten novel molecules were designed based on MLR QSAR model, then predicted with their ADME-Toxicity profiles and subsequently examined for their similarity to the drug candidates. Finally, two of the most active compounds (C37 and C39) were chosen for molecular docking and molecular dynamics (MD) investigations during 100 ns of MD simulation time in complex with the targeted protein of NMDA receptor (5EWJ.pdb). more...
- Published
- 2024
- Full Text
- View/download PDF
34. Design of Novel Membranes for the Efficient Separation of Bee Alarm Pheromones in Portable Membrane Inlet Mass Spectrometric Systems.
- Author
-
Armaković, Stevan, Ilić, Daria, and Brkić, Boris
- Subjects
- *
POLAR molecules , *POLYETHYLENE glycol , *MOLECULAR interactions , *MEMBRANE separation , *MULTILEVEL models - Abstract
Bee alarm pheromones are essential molecules that are present in beehives when some threats occur in the bee population. In this work, we have applied multilevel modeling techniques to understand molecular interactions between representative bee alarm pheromones and polymers such as polymethyl siloxane (PDMS), polyethylene glycol (PEG), and their blend. This study aimed to check how these interactions can be manipulated to enable efficient separation of bee alarm pheromones in portable membrane inlet mass spectrometric (MIMS) systems using new membranes. The study involved the application of powerful computational atomistic methods based on a combination of modern semiempirical (GFN2-xTB), first principles (DFT), and force-field calculations. As a fundamental work material for the separation of molecules, we considered the PDMS polymer, a well-known sorbent material known to be applicable for light polar molecules. To improve its applicability as a sorbent material for heavier polar molecules, we considered two main factors—temperature and the addition of PEG polymer. Additional insights into molecular interactions were obtained by studying intrinsic reactive properties and noncovalent interactions between bee alarm pheromones and PDMS and PEG polymer chains. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
35. Role of diffusion tensor imaging of extra ocular muscles and orbital fat in Graves's ophthalmopathy and relation to disease activity.
- Author
-
Hussein, Manar Mansour, Mohamed, Mohamed Ghonem, Mousa, Amany Abdel Hamid, Baiomy, Azza Abd El Baky, Abdel Razek, Ahmed Abd El Khalek, and El Ghani, Mohamed Roshdi Abd
- Subjects
IMMUNOGLOBULIN analysis ,MAGNETIC resonance imaging equipment ,EYE muscles ,EYE-sockets ,THYROID eye disease ,REFERENCE values ,ADIPOSE tissues ,CHEMISTRY ,THYROID gland function tests ,ENZYME-linked immunosorbent assay ,MAGNETIC resonance imaging ,SIGNAL processing ,DESCRIPTIVE statistics ,LONGITUDINAL method ,CASE-control method ,GRAVES' disease ,DATA analysis software ,SENSITIVITY & specificity (Statistics) ,BIOMARKERS - Abstract
Background: Graves' ophthalmopathy (GO) is one of the most common autoimmune inflammatory disorders affecting the orbit that characterized by swelling of extra ocular muscles (EOMs) and expansion of the orbital fat. Diffusion tensor imaging (DTI) could assess the microstructural integrity of tissue. We aimed at this study to assess the role of DTI in the evaluation of EOMs and orbital fat in GO and identify the relationship with disease activity. Results: Case–control study included 40 patients diagnosed as Graves' disease (20 active and 20 inactive) and 10 health control subjects underwent DTI. Low fraction anisotropy (FA) and high mean diffusivity (MD) of inferior rectus (IR), medial rectus (MR) and orbital fat in GO versus healthy control (HC), while high FA and high MD in active group versus inactive group. In order to differentiate between GO and HC; FA cutoff point of IR, MR& orbital fat were 0.46, 0.45 and 0.26 with sensitivity 98.8%,98.8% and 93.8% and specificity 95.0%, 95.0% and 85%, respectively. MD cutoff point for IR, MR and orbital fat 1.24, 1.27 and 1.275 with sensitivity 97.5%, 98.8% and 98.8% and specificity 95.0%, 95% and 95%, respectively. To differentiate between active and inactive GO; FA cutoff point of IR, MR and orbital fat were 0.35, 0.36 and 0.22 respectively with sensitivity 80.0%, 82.5% and 72.5% and specificity 95.0%, 85.0% and 65.0%, respectively. MD cutoff point for IR, MR and orbital fat were 1.58, 1.63 and 1.54 respectively with sensitivity 90.0%, 97.5% and 85.0%, and specificity 90.0%, 80.0% and 62.5%, respectively. Conclusions: DTI parameters (FA and MD) of EOMs and orbital fat are considered as crucial radiological biomarkers for diagnosis of GO and could quantitatively differentiate active form inactive disease. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
36. In silico insights into the design of novel NR2B-selective NMDA receptor antagonists: QSAR modeling, ADME-toxicity predictions, molecular docking, and molecular dynamics investigations.
- Author
-
El fadili, Mohamed, Er-rajy, Mohammed, Mujwar, Somdutt, Ajala, Abduljelil, Bouzammit, Rachid, Kara, Mohammed, Abuelizz, Hatem A., Er-rahmani, Sara, and Elhallaoui, Menana
- Subjects
ARTIFICIAL neural networks ,FRONTIER orbitals ,METHYL aspartate receptors ,MOLECULAR docking ,QSAR models - Abstract
Based on a structural family of thirty-two NR2B-selective N-Methyl-D-Aspartate receptor (NMDAR) antagonists, two phenylpiperazine derivatives labeled C37 and C39 were conceived thanks to molecular modeling techniques, as novel NMDAR inhibitors exhibiting the highest analgesic activities (of pIC
50 order) against neuropathic pain, with excellent ADME-toxicity profiles, and good levels of molecular stability towards the targeted protein of NMDA receptor. Initially, the quantitative structure-activity relationships (QSARs) models were developed using multiple linear regression (MLR), partial least square regression (PLSR), multiple non-linear regression (MNLR), and artificial neural network (ANN) techniques, revealing that analgesic activity was strongly correlated with dipole moment, octanol/water partition coefficient, Oxygen mass percentage, electronegativity, and energy of the lowest unoccupied molecular orbital, whose the correlation coefficients of generated models were: 0.860, 0.758, 0.885 and 0.977, respectively. The predictive capacity of each model was evaluated by an external validation with correlation coefficients of 0.703, 0.851, 0.778, and 0.981 respectively, followed by a cross-validation technique with the leave-one-out procedure (CVLOO) with Q2 cv of 0.785, more than Y-randomization test, and applicability domain (AD), in addition to Fisher's and Student's statistical tests. Thereafter, ten novel molecules were designed based on MLR QSAR model, then predicted with their ADME-Toxicity profiles and subsequently examined for their similarity to the drug candidates. Finally, two of the most active compounds (C37 and C39) were chosen for molecular docking and molecular dynamics (MD) investigations during 100 ns of MD simulation time in complex with the targeted protein of NMDA receptor (5EWJ.pdb). [ABSTRACT FROM AUTHOR] more...- Published
- 2024
- Full Text
- View/download PDF
37. MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.
- Author
-
Brueckner, Alexander C., Shields, Benjamin, Kirubakaran, Palani, Suponya, Alexander, Panda, Manoranjan, Posy, Shana L., Johnson, Stephen, and Lakkaraju, Sirish Kaushik
- Subjects
- *
MACHINE learning , *STRUCTURE-activity relationships , *LIGANDS (Biochemistry) , *CYCLIC peptides , *WORKFLOW - Abstract
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand–protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein–ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein–ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein–ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure–activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
38. Anti-corrosive properties of novel nano-B/N/S-doped and heterocycle-functionalized carbon dots: a combined DFT and MD simulation study.
- Author
-
Wu, Qiong, Li, Wanqiu, Zhou, Yunping, Hang, Zusheng, and Zhu, Weihua
- Abstract
In this work, two series of new potential nano-carbon dots (CDs) inhibitors with different sizes (series A: five rings; series B: ten rings), doped elements (B, N and S) and functional groups (–OH, –COOH, –CO-thiazole, –CO-imidazole) were designed. Their various anti-corrosive properties, corrosion inhibition efficiencies and mechanisms were investigated by DFT and MD. The results showed that the B-doping and S-doping could significantly improve the feedback bonding, while the N-doping can enhance the feedback and coordinate bonding. Most of CDs could be either solid nucleophiles or nucleophiles; their anti-corrosive parameters and adsorption energies are much better than common organic inhibitors, indicating their high value to be used as new inhibitors. Most CDs not have high ∆N (Fe) and high ∆N (Cu) and may be why some CDs can inhibit the corrosion to both Fe and Cu alloys. CDs in series B have better softness, ∆N and ∆E, than the corresponding ones in series A, suggesting the significant effect of the size, and it is necessary to consider this when using CD inhibitors. Finally, the N-doping, S-doping and B-doping influenced the structures, leading to different corrosion inhibition mechanisms. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
39. 6-Bromo quinazoline derivatives as cytotoxic agents: design, synthesis, molecular docking and MD simulation.
- Author
-
Emami, Leila, Hassani, Maryam, Mardaneh, Pegah, Zare, Fateme, saeedi, Maryam, Emami, Mina, Khabnadideh, Soghra, and Sadeghian, Sara
- Subjects
ERLOTINIB ,MOLECULAR docking ,QUINAZOLINE ,ANTINEOPLASTIC agents ,CELL lines ,SULFHYDRYL group - Abstract
Based on unselectively, several side effects and drug resistance of available anticancer agents, the development and research for novel anticancer agents is necessary. In this study, a new series of quinazoline-4(3H)-one derivatives having a thiol group at position 2 of the quinazoline ring (8a-8 h) were designed and synthesized as potential anticancer agents. The Chemical structures of all compounds were characterized by
1 H-NMR,13 C-NMR, and Mass spectroscopy. The antiproliferative activity of all derivatives were determined against two cancer cell lines (MCF-7 and SW480) and one normal cell lines (MRC-5) by the MTT method. Cisplatin, Erlotinib and Doxorubicin were used as positive controls. The results of in vitro screening showed that 8a with an aliphatic linker to SH group was the most potent compound with IC50 values of 15.85 ± 3.32 and 17.85 ± 0.92 µM against MCF-7 and SW480 cell lines, respectively. 8a indicated significantly better potency compared to Erlotinib in the MCF-7 cell line. The cytotoxic results obtained from testing compound 8a on the normal cell line, revealing an IC50 value of 84.20 ± 1.72 µM, provide compelling evidence of its selectivity in distinguishing between tumorigenic and non-tumorigenic cell lines. Structure–activity relationship indicated that the variation in the anticancer activities of quinazoline-4(3H)-one derivatives was affected by different substitutions on the SH position. Molecular docking and MD simulation were carried out for consideration of the binding affinity of compounds against EGFR and EGFR-mutated. The binding energy of compounds 8a and 8c were calculated at -6.7 and − 5.3 kcal.mol− 1 , respectively. Compounds 8a and 8c were found to establish hydrogen bonds and some other important interactions with key residue. The DFT analysis was also performed at the B3LYP/6–31 + G(d, p) level for compounds 8a, 8c and Erlotinib. Compound 8a was thermodynamically more stable than 8c. Also, the calculated theoretical and experimental data for the IR spectrum were in agreement. The obtained results delineated that the 8a can be considered an appropriate pharmacophore to develop as an anti-proliferative agent. [ABSTRACT FROM AUTHOR] more...- Published
- 2024
- Full Text
- View/download PDF
40. Theoretically and Experimentally Exploring the Inhibition Effect of Imidazole Sulfonic Acid Derivatives with Multiple Adsorption Sites in 1.0 mol/L HCl.
- Author
-
Wang, Pengjie, Fan, Lin, Song, Yuhao, Deng, Kuaihai, Guo, Lei, Li, Zhonghui, and Lin, Yuanhua
- Abstract
Corrosion inhibitors have played a huge role in daily life and industrial production. Imidazole and sulfonic acid groups have high corrosion inhibition capabilities. To further improve their excellent corrosion inhibition performance, two new sulfonic acid azole corrosion inhibitors (YM and ZM) were synthesized and the effect of carbon chain length on the imidazole sulfonic acid corrosion inhibitor was studied. The weight loss and electrochemical results indicated that the corrosion inhibition efficiency significantly increased with the increase of YM and ZM concentration. At 1.0 g/L of ZM, the corrosion inhibition efficiency of weight loss, EIS and Tafel were 95.02%, 86.61%, and 98.49%, respectively. Electrochemistry further indicated that ZM and YM could form a stable protective film on the surface of Q235 and increased the charge transfer resistance, thereby improving their corrosion inhibition efficiency and belong to cathodic corrosion inhibitors. SEM–EDS, FT-IR, and XPS confirmed that YM and ZM could effectively adsorb on the surface of Q235, and further demonstrated theories through density functional theory and molecular dynamics simulation. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
41. Efficient photocatalytic degradation of antibiotics by binary heterojunction complex boron subphthalocyanine bromide/bismuth oxychloride.
- Author
-
Ji, Mengting, Wang, Bing, Zheng, Zheng, Liu, Enzhou, Shi, Chuanhui, Wang, Chen, Tian, Bin, Ma, Haixia, Wei, Chaoyang, Zhou, Bo, and Li, Zhuo
- Subjects
- *
PHOTODEGRADATION , *HETEROJUNCTIONS , *ORGANIC water pollutants , *BISMUTH , *BENZENEDICARBONITRILE , *STACKING interactions , *PHTHALOCYANINE derivatives , *METAL phthalocyanines - Abstract
[Display omitted] The development of stable and efficient heterojunction photocatalysts for wastewater environmental purification exhibits a significant challenge. Herien, a promising binary heterojunction complex comprising boron subphthalocyanine bromide/bismuth oxychloride (SubPc-Br/BiOCl) was successfully synthesized using the hydrothermal method, which involved the self-assembled of SubPc-Br on the surface of BiOCl via intermolecular π-π stacking interactions to compose an electron-transporting layer. The photocatalytic efficiency of SubPc-Br/BiOCl for the degradation of tetracycline and the minocycline exhibited a substantial improvement of 29.14% and 53.72%, respectively, compared to the original BiOCl. Experimental characterization and theoretical calculations elucidated that the enhanced photocatalytic performance of the SubPc-Br/BiOCl composite photocatalysts stemmed from the S-scheme electron transport mechanism at the interface between BiOCl and SubPc-Br supramolecules, which broadened the visible light absorption range, increased the carrier molecular efficiency, and accelerated the carriers. Furthermore, molecular dynamic (MD) simulations provided insights into the action trajectories of the two semiconductors, revealing that the presence of SubPc-Br enhances the water and organic pollutant adsorption capabilities of the BiOCl surface within the supramolecular array system. In conclusion, the synthesis and analysis of the binary heterojunction complex SubPc-Br/BiOCl yield valuable insights into the efficient photocatalytic degradation of antibiotics, holding great promise for diverse environmental applications. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
42. Corrosion inhibition in 1M HCl of mild steel with Thymus leptobotrys Murb essential oil (TLMEO): electrochemical measurements and Density Function Theory (DFT) and Molecular Dynamics (MD) simulations.
- Author
-
Oubihi, A., Ouakki, M., Ech-chebab, A., Assiri, El H. El, Tarfaoui, K., Galai, M., Touhami, M. Ebn, Ouhssine, M., and Guessous, Z.
- Subjects
- *
MILD steel , *ESSENTIAL oils , *MOLECULAR dynamics , *DENSITY functional theory , *ADSORPTION isotherms , *CORROSION potential - Abstract
The corrosion inhibition of Thymus leptobotrys Murb essential oil (TLMEO) is evaluated for mild steel (M-S) in 1M HCl solution using electrochemical and surface analysis. Results showed that TLMEO acted as a potential corrosion inhibitor and shows the highest inhibition efficiency of 91.7% at 2g/l concentration. Electrochemical studies suggest that TLMEO acted as a mixed- and interface-type of corrosion inhibitor. The TLMEO inhibits metallic corrosion through an adsorption mechanism that follows Langmuir's adsorption isotherm model. The adsorption mechanism of corrosion inhibition was further supported using SEM–EDX, and surface studies. In addition, the anti-corrosion mechanism of the main TLMEO compounds was studied using computational techniques: Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations. Theoretical results were consistent with the experimental findings that were reported. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
43. Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics.
- Author
-
Doveiko, Daniel, Kubiak-Ossowska, Karina, and Chen, Yu
- Subjects
- *
MOLECULAR dynamics , *BINDING energy , *POLYCYCLIC aromatic hydrocarbons , *DIMERS , *STACKING interactions , *DENSITY functional theory - Abstract
π–π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π–π stacking energy values with reasonable precision. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
44. Oxidative Stress as a Target for Non-Pharmacological Intervention in MAFLD: Could There Be a Role for EVOO?
- Author
-
Seidita, Aurelio, Cusimano, Alessandra, Giuliano, Alessandra, Meli, Maria, Carroccio, Antonio, Soresi, Maurizio, and Giannitrapani, Lydia
- Subjects
OXIDATIVE stress ,VITAMIN E ,NON-alcoholic fatty liver disease ,FATTY liver ,MALONDIALDEHYDE ,MONOUNSATURATED fatty acids ,MEDITERRANEAN diet - Abstract
Oxidative stress plays a central role in most chronic liver diseases and, in particular, in metabolic dysfunction-associated fatty liver disease (MAFLD), the new definition of an old condition known as non-alcoholic fatty liver disease (NAFLD). The mechanisms leading to hepatocellular fat accumulation in genetically predisposed individuals who adopt a sedentary lifestyle and consume an obesogenic diet progress through mitochondrial and endoplasmic reticulum dysfunction, which amplifies reactive oxygen species (ROS) production, lipid peroxidation, malondialdehyde (MDA) formation, and influence the release of chronic inflammation and liver damage biomarkers, such as pro-inflammatory cytokines. This close pathogenetic link has been a key stimulus in the search for therapeutic approaches targeting oxidative stress to treat steatosis, and a number of clinical trials have been conducted to date on subjects with NAFLD using drugs as well as supplements or nutraceutical products. Vitamin E, Vitamin D, and Silybin are the most studied substances, but several non-pharmacological approaches have also been explored, especially lifestyle and diet modifications. Among the dietary approaches, the Mediterranean Diet (MD) seems to be the most reliable for affecting liver steatosis, probably with the added value of the presence of extra virgin olive oil (EVOO), a healthy food with a high content of monounsaturated fatty acids, especially oleic acid, and variable concentrations of phenols (oleocanthal) and phenolic alcohols, such as hydroxytyrosol (HT) and tyrosol (Tyr). In this review, we focus on non-pharmacological interventions in MAFLD treatment that target oxidative stress and, in particular, on the role of EVOO as one of the main antioxidant components of the MD. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
- View/download PDF
45. Advancing Tribological Understanding: Insights into In-Plane Wear and Edge Friction Mechanisms of Graphene and Its Derivatives
- Author
-
Jiang, Yilong, Chen, Lei, Tang, Chuan, Liu, Yangqin, Yan, Wenmeng, Wei, Liang, Qian, Linmao, Ceccarelli, Marco, Series Editor, Corves, Burkhard, Advisory Editor, Glazunov, Victor, Advisory Editor, Hernández, Alfonso, Advisory Editor, Huang, Tian, Advisory Editor, Jauregui Correa, Juan Carlos, Advisory Editor, Takeda, Yukio, Advisory Editor, Agrawal, Sunil K., Advisory Editor, Ciulli, Enrico, editor, and Ruggiero, Alessandro, editor more...
- Published
- 2024
- Full Text
- View/download PDF
46. A Molecular Dynamics Study to Compute Glass Transition Temperature of Neat Epoxy
- Author
-
Das, Pratyasha, Gupta, Nandini, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, and Sharma, Archana, editor more...
- Published
- 2024
- Full Text
- View/download PDF
47. Void Nucleation in a Through Silicon Via (TSV): Unraveling the Role of Tilt Grain Boundaries Through Atomistic Investigation
- Author
-
Shashaani, Armin, Sepehrband, Panthea, and The Minerals, Metals & Materials Society
- Published
- 2024
- Full Text
- View/download PDF
48. Robust Alignment Base on IKF for SINS/DVL Integrated Navigation System
- Author
-
Li, Jingshu, Zhu, Bing, Tian, Ge, Li, Zuohu, Jiang, De, Guo, Xia, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Yang, Changfeng, editor, and Xie, Jun, editor more...
- Published
- 2024
- Full Text
- View/download PDF
49. Sodium Ion Binding Pocket Mutations and Adenosine A2A Receptor Function
- Author
-
Massink, Arnault, Gutiérrez-de-Terán, Hugo, Lenselink, Eelke B., Ortiz Zacarías, Natalia V., Xia, Lizi, Heitman, Laura H., Katritch, Vsevolod, Stevens, Raymond C., and IJzerman, Adriaan P.
- Published
- 2015
- Full Text
- View/download PDF
50. Quantum Mechanics/Molecular Mechanics Simulations for Chiral-Selective Aminoacylation: Unraveling the Nature of Life
- Author
-
Tadashi Ando and Koji Tamura
- Subjects
QM/MM ,MD ,transition state: homochirality ,aminoacylation ,tRNA ,origin of life ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Biological phenomena are chemical reactions, which are inherently non-stopping or “flowing” in nature. Molecular dynamics (MD) is used to analyze the dynamics and energetics of interacting atoms, but it cannot handle chemical reactions involving bond formation and breaking. Quantum mechanics/molecular mechanics (QM/MM) umbrella sampling MD simulations gives us a significant clue about transition states of chemical reactions and their energy levels, which are the pivotal points in understanding the nature of life. To demonstrate the importance of this method, we present here the results of our application of it to the elucidation of the mechanism of chiral-selective aminoacylation of an RNA minihelix considered to be a primitive form of tRNA. The QM/MM MD simulation, for the first time, elucidated the “flowing” atomistic mechanisms of the reaction and indicated that the L-Ala moiety stabilizes the transition state more than D-Ala, resulting in L-Ala preference in the aminoacylation reaction in the RNA. The QM/MM method not only provides important clues to the elucidation of the origin of homochirality of biological systems, but also is expected to become an important tool that will play a critical role in the analysis of biomolecular reactions, combined with the development of artificial intelligence. more...
- Published
- 2024
- Full Text
- View/download PDF
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.