Article
Biochemical Research Methods
Krishna Chaturvedi, Caroline S. Anthony, Pankaj Pandey, Robert J. Doerksen, Murrell Godfrey
Summary: This study evaluated the interactions between the CB1 receptor and ligands from the JWH synthetic cannabinoid family, as well as newly designed JWH-like virtual compounds. The results revealed important structural characteristics that influenced the predicted CB1 binding affinity, including the carbonyl group and the length of the alkyl chain.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Weijian Wang, Yong Feng, Xiaoyang Li
Summary: In this study, the mechanical properties of recycled concrete (RC) were improved through two different modification methods. The results showed that the compressive and shear strength of RC modified by Silane Coupling Agent (KH560)/Ethylene vinyl acetate copolymer (EVA) was higher than that of RC modified by EVA alone. The effects of separate and co-modification on RC were analyzed through multi-scale methods, and the results provided insights into the macro-mechanical properties, microstructure, chemical composition, and molecular mechanism of the modified RC.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Xue-Fen Zhang, Ning Wang, Xu-Dong Li, Xiang Li, Chen-Xiang Wang
Summary: In this study, the protection behaviors of superhydrophobic dodecyltrimethoxysilane for mild steel were explored using molecular dynamics simulation. The results showed that the absorption orientations of the silane and the wetting behaviors of water clusters played important roles in the protection mechanism. The superhydrophobic silane film exhibited a repulsive effect on water droplets, confining corrosive species to specific regions and reducing their diffusion coefficient, thereby improving the corrosion protection of the underlying metal substrate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Biyu Xu, Luguang Liang, Yirong Jiang, Zuguo Zhao
Summary: This study investigates the underlying mechanisms of resistance to ibrutinib caused by the BTK L528W mutation using bioinformatics analysis and molecular dynamics simulations. The results demonstrate that the L528W mutation reduces BTK stability, decreases binding affinity, and leads to drug resistance and potential disease recurrence.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
V. Nagarajan, M. Vaishnavi, R. Bhuvaneswari, R. Chandiramouli
Summary: Amino acids are essential for protein synthesis and their deficiency can affect sleep and mood. This study investigates the adsorption properties of alanine and asparagine amino acids on one-dimensional chair graphene nanotubes. The results show that alanine and asparagine are physically adsorbed on the nanotubes, which act as electron donors. Additionally, changes in the band gap and electron density of the graphene nanotubes are observed.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Chemistry, Multidisciplinary
Dayanni D. Bhagwandin, John H. Dunlap, Ly D. Tran, Alexander Reidell, Drake Austin, Amelia A. Putnam-Neeb, Morgan Loveday, Rahul Rao, Luke A. Baldwin, Nicholas R. Glavin
Summary: Flow systems allow for in-line synthesis and processing of organic materials, offering advantages in high-throughput and scalability. In this study, a highly crystalline TAPB-OHPDA covalent organic framework (COF) was directly crystallized under continuous flow conditions in just 30 minutes. BET surface analysis showed that high surface areas above 1700 m2 g-1 can be achieved in 2 hours, resulting in a processing time 36 times faster than most solvothermal methods. The findings provide foundational knowledge for COF syntheses under packed-bed flow conditions and demonstrate an opportunity to accelerate the formation and processing of highly crystalline COF materials.
Article
Chemistry, Multidisciplinary
Jiewen Jiang, Yun Dai, Jiamin Shang, Zhen Zhang, Liangbi Su, Maojie Cheng, Dunlu Sun, A. Stupakiewicz, Anhua Wu
Summary: In this study, Bi, Mn co-doped Y3Fe5O12 films with good crystallinity and magneto-optical properties were prepared. These films have pseudomorphic structures on the substrate and exhibit high perpendicular magnetic anisotropy. It was found that lattice mismatch affects the stress-induced magnetic anisotropy, while the Mn3+ content regulates the magnetostriction effect on the perpendicular magnetic anisotropy.
Correction
Chemistry, Multidisciplinary
Y. Maximilian Klein, Alessandro Prescimone, Mateusz B. Pitak, Simon J. Coles, Edwin C. Constable, Catherine E. Housecroft
Summary: Correction for the article "Constructing chiral MOFs by functionalizing 4,2',4''-terpyridine with long-chain alkoxy domains: examples of dia nets" by Y. Maximilian Klein et al., which was published in CrystEngComm, 2016, 18, 4704-4707.
Article
Chemistry, Multidisciplinary
Yaohui Liu, Yu Tang, Yonggui Tao, Ying Zhang, Lanxian Shen, Wen Ge, Shukang Deng
Summary: This study focuses on the effect of Cu doping on the thermoelectric properties of BiSbTe3 (BST) alloys. Cu doping significantly improves the crystal quality and density of the alloy, thereby increasing the material's mobility and reducing the resistivity. However, it also introduces dislocations and lattice distortions. The highly doped samples contain Cu2Te and BST superlattice structures, which further enhance the scattering of heat transfer phonons, significantly reducing the lattice thermal conductivity. Cu-doped samples exhibit extremely low lattice thermal conductivity, leading to a significant increase in their ZT values. These findings highlight the potential application of Cu-doped BiSbTe3 alloys in room temperature refrigeration and power generation.
Article
Chemistry, Multidisciplinary
Anton P. Novikov, Alexey V. Safonov, Konstantin E. German, Mikhail S. Grigoriev
Summary: L-Histidinium perrhenate and pertechnetate were synthesized and their crystal structures were studied. This work presents the first examples of tetrahedral transition metal anions with histidine and describes a new type of interaction between ions.
Article
Chemistry, Multidisciplinary
Chunbo Liu, Jianchun Guo, Wei Liu, Linjie Yang
Summary: This paper investigates the effects of viscous, elastic, and dielectric parameters on the electrohydrodynamic performance of a positive nematic liquid crystal 5CB using the computational fluid dynamics (CFD) method. The study establishes governing and constitutive equations and explores the relationship between micro-flow velocity and the angular velocity of the 5CB directors. The results are validated through micro-particle image velocimetry (micro-PIV) experiments, providing a theoretical foundation for further research and application of liquid crystalline microfluidic driving methods.
Article
Crystallography
Kangyao Wang, Leng Chen
Summary: In this study, we investigated the non-isothermal crystallization kinetics of Sb70Se30 thin films. The results revealed a multi-step crystallization mechanism, with the crystallization activation energy decreasing as the crystallization fraction increases. The crystallization mechanism shifted from three-dimensional growth to three-dimensional and two-dimensional growth as the crystallization fraction increased. Furthermore, the Sb70Se30 thin film exhibited excellent data retention capability.
JOURNAL OF CRYSTAL GROWTH
(2023)
