Article
Chemistry, Analytical
Maryam Mehrdadian, Sadegh Khazalpour, Ameneh Amani
Summary: The electrochemical reaction of 4-ethynylaniline with sodium azide in buffered solutions at different pH values was investigated for the first time. A triazole ring was successfully synthesized through a series of electrochemical oxidations and chemical reactions, using a non-catalytic procedure at room temperature.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Maria Assunta Chiacchio, Daniela Iannazzo, Salvatore Giofre, Roberto Romeo, Laura Legnani
Summary: In this paper, a mechanistic study of RuO4-catalyzed oxidation on 2-methylisoxazolidine was conducted using computational methods. The investigation revealed that the oxidation reaction occurs in two steps involving double H-transfer. The study also found that all carbon atoms near the heteroatoms in the isoxazolidine system can undergo oxidation, with the formation of an ion pair leading to the preferred product N-methylisoxazolidin-3-one.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Giorgio Molteni, Alessandro Ponti
Summary: In this study, the accuracy of predicting the regioselectivity of uncatalyzed thermal azide 1,3-DCs using DFT calculations was investigated. Benchmark data was established and compared with results obtained using density functional approximations (DFAs). The study identified the key features for accurate regioselectivity and suggested potential improvements for future research.
Review
Chemistry, Multidisciplinary
Steven E. Beutick, Pascal Vermeeren, Trevor A. Hamlin
Summary: The 1,3-dipolar cycloaddition reaction has proven immensely useful in organic, material, and biological chemistry, with metal catalysis and predistortion or electronic tuning of the dipolarophile enhancing reactivity. Quantum chemical calculations are critical for understanding physical factors controlling reactivity and selectivity, and design principles derived from in silico calculations are invaluable for tailored reactivity of new dipolarophiles.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Chemistry, Organic
Jian-Bin Lu, Shu-Yuan Liang, Wu-Tao Gui, Zhi-Chao Chen, Wei Du, Ying-Chun Chen
Summary: A relay catalytic protocol utilizing pyrrolidine and palladium catalysis has been developed for the asymmetric synthesis of 1,3-diamine derivatives from 3-substituted 1,3-dienes, sulfuric diamide, and aldehydes. This one-pot, three-component reaction offers the advantages of high atom step economy and operational simplicity, providing an efficient and straightforward access to valuable 1,3-diamines containing quaternary and tertiary stereogenic centers with moderate to good enantioselectivity.
Article
Chemistry, Multidisciplinary
Luis R. Domingo, Mar Rios-Gutierrez, Rishikesh Chulan, M. H. H. Mahmoud, Mohamed M. Ibrahim, Salah M. El-Bahy, Lydia Rhyman, Ponnadurai Ramasami
Summary: The study investigated the role of cyclopropane substitution on the ethylene in zw-type 32CA reactions, showing that it does not significantly affect the reactivity or transition state structure but decreases activation enthalpy and ortho regioselectivity.
Article
Chemistry, Organic
Luis R. Domingo, Karolina Kula, Mar Rios-Gutierrez, Radomir Jasinski
Summary: The carbenoid-type 32CA reaction between 1,1-difluoroated azomethine ylide (DFAY) and phenylpropynal was studied using molecular electron density theory (MEDT). The study found that DFAY exhibits supernucleophilic character, leading to a highly exothermic reaction with total chemo- and regioselectivity. The reaction follows a non-concerted two-stage one-step mechanism involving nucleophilic attack of the carbenoid carbon of DFAY on the electrophilic carbonyl carbon of the ynal.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Nicolaj Inunnguaq Jessen, Joseph A. Izzo, Marek S. Modlinski, Giulio Bertuzzi, Karl Anker Jorgensen
Summary: The development of higher-order cycloadditions has been limited due to the need for highly conjugated and reactive pi-systems. Recent research shows that organocatalysis can be an efficient mediator to overcome these challenges. Computational studies have also found that the impact of benzofusions on higher-order cycloadditions can be explained by changes in energy barriers.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Zhenni Zhao, Zhi Ou, Subarna Jyoti Kalita, Feng Cheng, Qian Huang, Yangyi Gu, Yuhao Wang, Yan Zhao, Yiyong Huang
Summary: This paper reports the first example of a stereoconvergent reaction involving 1,3-dipolar cycloaddition of nitrile oxides and nitrile imines with electron-deficient olefins. The reaction produces compounds with multiple stereogenic centers and exhibits excellent regio- and diastereoselectivities. Through control experiments and calculations, the possibility of thermodynamically stable diastereomers formation during the reaction is ruled out, and a stepwise mechanism is proposed.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Organic
Dennis Svatunek, Thomas Hansen, Kendall N. Houk, Trevor A. Hamlin
Summary: The Lewis base F- catalyzes the 1,3-dipolar cycloaddition between CO2 and nitrilimines by activating the nitrilimine and enhancing the rate of the reaction. The strength of primary orbital interactions between the reactants is the origin of this catalysis. The Lewis base activated nitrilimine-F- has high-lying filled FMOs, which promote a rapid nucleophilic attack and overall cycloaddition with CO2.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Sha Li, Yahan Sun, Xiaofang Li, Oskar Smaga, Sebastian Koniarz, Marcin Stepien, Piotr J. Chmielewski
Summary: A 1,3-cycloaddition reaction between 2-(tert-butyl)-8H-isoquinolino[4,3,2-de]phenanthridin-9-ium chloride and Ni-II norcorrole in the presence of base has been demonstrated to yield a family of chiral derivatives fused with pyrrole subunits of the macrocycle. Dehydrogenation of the cycloaddition products leads to dibenzoullazine ortho-fused antiaromatic porphyrinoids.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Pan-Pan Chen, Pengchen Ma, Xue He, Dennis Svatunek, Fang Liu, Kendall N. Houk
Summary: This study examines the ambiphilic nature of Huisgen's phenyl azide cycloadditions based on Reiner Sustmann's seminal discoveries, using density functional calculations and energy decomposition analyses to understand the control of reactivity. The research shows that Sustmann's use of dipolarophile ionization potential is a powerful predictor of reactivity, and modern distortion-accelerated dipolarophiles fit into orbital energy criteria used to understand cycloaddition reactivity. It is revealed that this simple indicator of reactivity is a strong predictor of reaction rates controlled by a combination of various factors such as distortion energies, charge transfer, closed-shell repulsion, and electrostatic effects.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Lorand Kiss, Jorge Escorihuela
Summary: Density functional theory calculations were used to investigate the reactivity and regioselectivity of 1,3-dipolar cycloaddition reactions. The calculated activation free energies reproduced the experimentally observed product ratios. Both electronic and steric effects influenced the regioselectivities.
Article
Chemistry, Organic
Zhenjie Qi, Shaozhong Wang
Summary: A copper(II)-catalyzed protocol has been developed for the construction of trans-configured beta-lactams and spirocyclic beta-lactams from oximes and methyl propiolate, with excellent substrate flexibility and diastereoselectivity (up to >99:1 dr). In situ FT-IR mechanistic experiments suggest that ketene species may be involved in the formation of beta-lactams.
Review
Biochemistry & Molecular Biology
P. Rahul, Joice Thomas, Wim Dehaen, Jubi John
Summary: This review summarizes several reports on the synthesis of fused 1,2,3-triazole containing scaffolds using a sequential multicomponent reaction-intramolecular azide-alkyne cycloaddition approach. The reactions were carefully designed to incorporate azide and alkyne functionalities in the MCR product, which was then subjected to IAAC. The review is divided into two sections based on the number of components in the multicomponent reaction, and provides a critical discussion and analysis of the advantages and disadvantages of each methodology.
Article
Chemistry, Organic
Soukaina Chehab, Youssef Merroun, Tourya Ghailane, Rachida Ghailane, Said Boukhris, Abdelaziz Souizi
Summary: This study presents a simple procedure for preparing cadmium pyrophosphate by modifying mono-ammonium phosphate with cadmium chloride. The obtained support was characterized using various microscopic and spectroscopic methods. The catalytic activity of Cd2P2O7 was evaluated in the synthesis of 2,3-dihydroquinazolin-4(1H)-one derivatives, showing high efficiency, excellent yields, and recyclability.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Chemistry, Physical
M. E. Belghiti, F. Benhiba, N. Benzbiria, Chin-Hung Lai, S. Echihi, M. Salah, A. Zeroual, Y. Karzazi, A. Tounsi, K. Abbiche, S. Belaaouad, H. Elalaoui-Elabdallaoui, Y. Naimi
Summary: Four Trizaoles were investigated as corrosion inhibitors on mild steel in strong H3PO4 medium, and their inhibition activities were evaluated by weight loss measurements. The results showed that TR3 exhibited the highest inhibition activity, and the hydration energy was found to be a valuable descriptor for inspecting the inhibition performance of organic compounds.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Multidisciplinary
Ossama Daoui, Noureddine Mazoir, Mohamed Bakhouch, Mohammed Salah, Ahmed Benharref, Azucena Gonzalez-Coloma, Souad Elkhattabi, Mohamed El Yazidi, Samir Chtita
Summary: In this study, computational methods were used to evaluate the insecticidal properties and predict the structures of triterpene derivatives. The developed 3D-QSAR models showed excellent statistical results and were used to design new molecules with potential antibacterial and insecticidal activities. Molecular docking tests confirmed the hypothesis and identified three molecules with greater stability than the reference molecule inside the targeted receptors.
STRUCTURAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Said Kerraj, Mohammed Salah, Samir Chtita, Mohammed El Idrissi, Said Belaaouad, Moutaabid Mohammed, Nivedita Acharjee, Najia Komiha
Summary: This study investigates nine mononuclear Ru, Rh, and Ir half sandwich complexes used in dye-sensitized solar cells. The researchers calculated the structural, electronic, and optical properties of these complexes and compared the results with experimental data, finding good agreement.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2022)
Article
Chemistry, Organic
Soukaina Chehab, Youssef Merroun, Rachida Ghailane, Said Boukhris, Abdelaziz Souizi
Summary: In this paper, Na2Ca(HPO4)(2) was used as a heterogeneous catalyst for the first time, achieving efficient and green synthesis of 1,8-dioxo-octahydroxanthenes and biscoumarin derivatives. The method shows several advantages, including avoiding toxic solvents and catalysts, simple handling, mild conditions, easy recovery, and catalyst reuse.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Chemistry, Multidisciplinary
Achraf El Hallaoui, Youssef Merroun, Soukaina Chehab, Rachida Ghailane, Abdelaziz Souizi
Summary: 2,4,6-trisubstituted pyridines are important heterocyclic compounds widely used in pharmaceutical industry, posing a crucial challenge to organic chemists for their preparation. In this study, we present a highly efficient one-step synthesis of triarylpyridine using Al/Ag3PO4 phosphate bimetallic catalysis from the condensation of acetophenone derivatives, aryl aldehydes, and ammonium acetate under mild and environmentally friendly conditions. This methodology offers advantages of excellent yields, shorter reaction times, and remarkable reusable activity of the catalyst. Compared to previous methods, our procedure allows a more flexible, straightforward, faster, and efficient preparation of substituted pyridines.
MONATSHEFTE FUR CHEMIE
(2023)
Article
Chemistry, Multidisciplinary
Ferraa Soumya, Merroun Youssef, Barebita Hanane, Chehab Soukaina, Baach Badr, Nimour Abderrazak, Ghailane Rachida, Souizi Abdelaziz, Guedira Taoufiq
Summary: New Bi17Ba0.45V2.1-xPxO31.2 composites were synthesized via a solid-state method using vanadium oxide (V2O5), barium carbonate (BaCO3), bismuth oxide (Bi2O3), and ammonium hydrogen phosphate ((NH4)2HPO4). Characterization results showed that the composites crystallize in the cubic system with Fm3m space group. The composites exhibit excellent catalytic efficiency in the synthesis of biscoumarins derivatives, with high yields and short reaction times.
RESULTS IN CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tarik Boutadghart, Rachida Ghailane
Summary: The [4+2] cycloaddition reactions between furan and three substituted alkynes have been studied using the MEDT approach. The reactivity indices, reaction pathways, and activation energies have been calculated. The reaction is regioselective and follows a non-concerted two-stage one-step molecular mechanism.
JOURNAL OF MOLECULAR MODELING
(2023)
Article
Chemistry, Multidisciplinary
Nabil Nor, Soukaina Zahm, Noureddine Mazoir, Habib El Alaoui El Abdallaoui, Ahmed Benharref, Mohamed Bakhouch, Redouane Mghaiouini, Salah Mohammed
Summary: In this study, molecular docking and dynamic simulation were used to investigate the potential inhibition of natural terpenoids and designed analogs against SARS-CoV-2. The natural terpenoids were isolated from Euphorbia officinarum and Euphorbia royleana. The Mpro protein was selected as the target for this study. The results showed that the designed analogs exhibited excellent binding energies and promising drug-likeness characteristics, suggesting their potential as drug candidates against SARS-CoV-2.
JOURNAL OF THE INDIAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Youssef Merroun, Soukaina Chehab, Achraf El Hallaoui, Taoufiq Guedira, Said Boukhris, Rachida Ghailane, Abdelaziz Souizi
Summary: This study introduces a mono-ammonium phosphate-based heterogeneous catalyst with simplicity, reusability, and recoverability, well-suited for multicomponent reactions. The catalyst was thoroughly characterized using FT-IR, XRD, SEM, and EDX. Employing this catalyst in a one-pot multicomponent approach enables efficient synthesis of xanthene derivatives. The results demonstrate the impressive performance and stability of SnP2O7 as a heterogeneous catalyst, with yields ranging from good to excellent and no significant decrease after five cycles.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Chemistry, Physical
A. Khannous, S. Jorio, N. Acharjee, Mohammad Azam, K. Min, M. Salah
Summary: The [3 + 2] cycloaddition reaction between benzonitrile oxide BNO and 5-methylenehydantoin (MH) was studied using the MEDT perspective at the DFT/B3LYP/6-31 + g(d,p) level of theory. The results showed that this reaction had a zwitterionic character based on topological analysis of the ELF, and the non-polar character was confirmed by GEDT calculations at the transition states. The energetically predicted regioselectivity and facial selectivity towards the anti isomer agreed well with the experimental outcome.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Achraf El Hallaoui, Youssef Merroun, Soukaina Chehab, Said Boukhris, Hicham Hassoune, Rachida Ghailane, Abedelaziz Souizi
Summary: This study presents a new environmentally sustainable catalytic method for the synthesis of symmetrically substituted pyridine derivatives and substituted alkene derivatives using zinc phosphate (Zn-3(PO4)(2)& BULL;4H(2)O) as a non-toxic and green heterogeneous catalyst. Trisubstituted pyridine derivatives were prepared with excellent yields (82-94%) via a three-component, one-pot synthesis of aromatic aldehydes, substituted acetophenones, and ammonium acetate in the presence of 0.4 mol% of Zn-3(PO4)(2)& BULL;4H(2)O using an ethanol/water (4/1) mixture as the solvent, while substituted alkenes were synthesized with up to 90% yield using the prepared catalyst. The experimental results demonstrate the efficiency of these new catalytic syntheses that present various advantages such as short reaction times, excellent yields, and an environmentally friendly profile.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Proceedings Paper
Materials Science, Multidisciplinary
Redouane Mghaiouini, Mortadi Abdelhadi, Dennoun Saifaoui, Mohammed Salah, Elmlouky Abderrahmane, El Ghaouti Chahid, Zouhair El Jouad, Khalid Kandoussi, Rkia Zari, Mohamed Monkade, Abdeslam El Bouari
Summary: Experimental results show that the evaporation rate of salt water slightly increased under the low frequency electromagnetic fields, possibly due to the breaking of hydrogen bonds or increased surface induction. Further research is needed to investigate the impact of magnetic field on thermal behavior.
MATERIALS TODAY-PROCEEDINGS
(2022)
Proceedings Paper
Materials Science, Multidisciplinary
Redouane Mghaiouini, Mortadi Abdelhadi, Youssef Hairch, Dennoun Saifaoui, Mohammed Salah, Elmlouky Abderrahmane, El Ghaouti Chahid, Meryem Bensemlali, Fouad Belhora, Mahmoud El Mouden, Mohamed Monkade, Abdeslam El Bouari
Summary: Experiment tests were conducted to investigate the impact of a low-frequency electromagnetic field of 40 mT on the freezing and cooling temperature of salt water. The results showed a slight decrease in the freezing and cooling temperature of magnetized saline water compared to untreated saline water. Possible explanations include the disruption of hydrogen bonds and the presence of Na+ and Cl- ions, which result in the dissociation of H2O molecule clusters. The Lorentz force may also contribute to the increase in surface induction, leading to a reduction in surface tension and a change in the thermal behavior of magnetized saline water.
MATERIALS TODAY-PROCEEDINGS
(2022)
Article
Multidisciplinary Sciences
Redouane Mghaiouini, Mohammed Salah, Mohamed Monkade, Abdeslam El Bouari
Summary: The phenomenon of water magnetization by an electromagnetic field poses a major challenge in current research. Factors such as temperature, salinity, and velocity significantly influence the magnetization time of water, while pH has no significant effect.
ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING
(2022)
Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
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
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
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
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
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
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
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
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
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
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
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
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)
