Article
Chemistry, Organic
Yohannan Sheena Mary, Yohannan Shyma Mary
Summary: Cocrystals of sulfathiazole with theophylline and sulfanilamide have been investigated for their potential applications in crystal engineering and pharmaceutical chemistry. Various analyses such as natural bond orbital, nonlinear optical properties, and molecular geometries were conducted to understand the molecular structure and potential charge transfer within the cocrystals. Furthermore, the study also explored the suitability of these cocrystals for use in dye-sensitized solar cells and potential inhibitory effects in drug development through docking studies.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Chemistry, Organic
D. Jagadeeswara Rao, Y. Sheena Mary, Y. Shyma Mary, K. S. Resmi, Renjith Thomas
Summary: The quantum chemical calculation and experimental spectral study of 9-methylanthracene and 2,3-dimethylanthracene molecules were conducted, showing good agreement between theoretical frequencies and experimental values. Additionally, the research also included molecular structure analysis, nonlinear optical studies, and molecular docking studies.
POLYCYCLIC AROMATIC COMPOUNDS
(2021)
Article
Biochemical Research Methods
P. Pounraj, P. Ramasamy, M. Senthil Pandian
Summary: The study systematically investigates 10-Hexylphenoxazine-based dyes with A-(pi)(n)-D-(pi)(n)-A architecture for DSSC application using DFT and TD-DFT. The electronic and optical properties of the designed sensitizers are analyzed, with a focus on pi-spacers configurations and their effect on charge separation and free energy properties.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Chemistry, Physical
Jared R. Williams, Nicolas Tancogne-Dejean, Carsten A. Ullrich
Summary: Time-dependent density-functional theory (TDDFT) is an efficient method for calculating optical spectra, providing insight into exciton dynamics by obtaining exciton wave functions and understanding the formation and dissociation of excitons in real time.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Organic
Y. Sheena Mary, Tugba Ertan-Bolelli, Renjith Thomas, Akhil R. Krishnan, Kayhan Bolelli, Esin Nagihan Kasap, Tijen Onkol, Ilkay Yildiz
Summary: The energetically stable conformation and optical properties of three organic compounds were investigated. The compounds show potential for development as inhibitor molecules of Topoisomerase II enzyme, with PTPS having potential applications in the design of new DSSCs due to its high light harvesting efficiency.
POLYCYCLIC AROMATIC COMPOUNDS
(2021)
Article
Chemistry, Physical
Ying Gao, Chenglin Sun, Tan Su
Summary: In this study, the stability of TADF devices was improved by introducing tert-butyl and phenyl into the peripheral position of carbazole. The TADF property was judged through specific HOMO-LUMO overlap calculation. By designing positional isomers combining tert-Butyl-substituted carbazole with different acceptors, potential TADF emitters were identified based on HOMO-LUMO overlap calculation. The results suggest that HOMO-LUMO overlap can be used to identify promising synthetic motifs for TADF candidates among structural isomers.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Multidisciplinary
Kaijin Liu, Jiaxue Niu, Ling Liu, Fangzhen Tian, Hongmei Nie, Xiaoyu Liu, Ke Chen, Ruoli Zhao, Si Sun, Menglu Jiao, Maoye Tian, Xinyu Sun, Lanfei Niu, Xinyi Sun, Hao Wang, Wei Long, Liefeng Feng, Xiaoyu Mu, Xiao-Dong Zhang
Summary: Chitosan-coated Se nanozymes were developed with 23-fold higher antioxidative activity than Trolox, and bovine serum albumin-coated Te nanozymes showed stronger prooxidative biocatalytic effects. This work provides a new strategy for improving the catalytic activities of Se and Te nanozymes.
Article
Chemistry, Physical
Ravi Trivedi, Vikash Mishra
Summary: In this study, the structural stability and electronic properties of transition metal doped germanium cages were investigated using density functional theory. It was found that 4d transition metals result in more stable structures compared to 3d transition metals, and different charge transfer mechanisms were observed.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Prabhat Ranjan, Brotati Chakraborty, Tanmoy Chakraborty
Summary: A detailed computational analysis is carried out for various acridine derivatives using conceptual density functional theory (CDFT). The study reveals that these compounds exhibit pronounced electron acceptor behavior in the excited state, and acridone has the highest HOMO-LUMO energy gap, indicating the feasibility of one-way electron transfer.
MOLECULAR DIVERSITY
(2023)
Article
Chemistry, Physical
Sania Bibi, Sehrish Sarfaraz, Muhammad Yar, Muhammad Iqbal Zaman, Abdul Niaz, Ayesha Khan, Muhammad Ali Hashmi, Khurshid Ayub
Summary: Density functional theory and Time Dependent Density functional theory calculations were used to study the interaction between sulfide ion and different functionalized single wall carbon nanotubes. The results showed that the sidewall functionalized COOH+NH2-SWCNT has a higher sensing ability towards sulfide ion.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Materials Science, Multidisciplinary
Behzad Babaei Moghadam, Ebrahim Sadeghi, Abbas Ali Rostami, Soheil Fazli
Summary: In this study, the adsorption of CS2 and COF2 molecules on the surface of C20 and C19X (X = Zn, Co, Sc) clusters was examined using DFT calculations and the B3LYP functional. The results were investigated in terms of net charge transfer, frontier orbitals, binding energy, electrical and thermodynamic properties. Doping C20 nanocages with (Zn, Co, Sc) transition metal atoms improved the binding energy, while the best binding energy was observed for COF2 adsorbed on C19Sc. The thermodynamic analyses showed that all the adsorption processes examined were exothermic.
MATERIALS TODAY COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Austin Biaggne, William B. Knowlton, Bernard Yurke, Jeunghoon Lee, Lan Li
Summary: The properties of dye monomers greatly influence their aggregation ability and exciton dynamics. By engineering dyes with specific substituents, optimal key properties like hydrophobicity and dipole moments can be achieved. This study found that electron withdrawing substituents significantly affect the solvation energy of the dye, while various pairs of substituents can enhance the static dipole difference.
Article
Chemistry, Physical
Jia-Ming Zhang, Huai-Qian Wang, Hui-Fang Li, Biao Xie, Chao Han, Long-Ying Jiang
Summary: The structure and growth of Lu-doped germanium clusters were investigated using photoelectron spectroscopy and density functional theory. The ground states of the anionic LuGen- clusters were verified by comparing simulated PES with experimental results. The pentagonal bipyramid shape was observed as the basic framework for the growth process of LuGen-.
Article
Biochemical Research Methods
Sana Fatima, Asim Mansha, Sadia Asim
Summary: In this study, the spectral behavior and molecular structure of 7-Hydroxycoumarin were investigated using various analytical methods. Excellent agreement was found between measured and estimated frequency ranges, and the solvatochromic effect on the spectral behavior was observed.
JOURNAL OF FLUORESCENCE
(2022)
Article
Chemistry, Physical
Abdul Majid, Maryam Sana, Salah Ud-Din Khan, Ashfaq Ahmad
Summary: First principles methods were used to design new metal-free organic dyes for improving photoinjection in dye sensitized solar cells. Structural modifications, including the addition of benzothiadiazole and pyridine, were made to shift the absorption spectrum of the dyes. Analysis revealed that dyes containing triarylamine in the donor assembly had the highest light harvesting efficiencies. Adsorption of dyes on TiO2 particles was used to model the photoinjection process, showing that dyes with benzothiadiazole in the pi-bridge had the smallest injection energies. The investigation of UV-visible spectra of dye-semiconductor complexes explored the suitability of the dyes for practical applications in DSSCs.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
V. Sivasubramani, Jesby George, M. Senthil Pandian, P. Ramasamy, P. Pounraj, K. K. Maurya, D. Sajan
NEW JOURNAL OF CHEMISTRY
(2018)
Article
Physics, Multidisciplinary
V. Mohankumar, P. Pounraj, M. Senthil Pandian, P. Ramasamy
BRAZILIAN JOURNAL OF PHYSICS
(2019)
Article
Biochemistry & Molecular Biology
P. Pounraj, V. Mohankumar, M. Senthil Pandian, P. Ramasamy
JOURNAL OF MOLECULAR MODELING
(2018)
Article
Materials Science, Multidisciplinary
N. Santhosh, S. R. Sitaaraman, P. Pounraj, R. Govindaraj, M. Senthil Pandian, P. Ramasamy
Article
Chemistry, Physical
V. Mohankumar, P. Pounraj, M. Senthil Pandian, P. Ramasamy
JOURNAL OF MOLECULAR STRUCTURE
(2019)
Article
Chemistry, Physical
V. Mohankumar, P. Pounraj, M. Senthil Pandian, P. Ramasamy
Article
Biochemical Research Methods
P. Pounraj, P. Ramasamy, M. Senthil Pandian
Summary: The study systematically investigates 10-Hexylphenoxazine-based dyes with A-(pi)(n)-D-(pi)(n)-A architecture for DSSC application using DFT and TD-DFT. The electronic and optical properties of the designed sensitizers are analyzed, with a focus on pi-spacers configurations and their effect on charge separation and free energy properties.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Proceedings Paper
Physics, Condensed Matter
P. Pounraj, M. Senthil Pandian, P. Ramasamy
DAE SOLID STATE PHYSICS SYMPOSIUM 2019
(2020)
Proceedings Paper
Physics, Applied
V. Mohankumar, P. Pounraj, M. Senthil Pandian, P. Ramasamy
DAE SOLID STATE PHYSICS SYMPOSIUM 2018
(2019)
Proceedings Paper
Physics, Applied
P. Pounraj, V. Mohankumar, M. Senthil Pandian, P. Ramasamy
DAE SOLID STATE PHYSICS SYMPOSIUM 2018
(2019)
Proceedings Paper
Green & Sustainable Science & Technology
P. Pounraj, V. Mohankumar, M. Senthil Pandian, P. Ramasamy
INTERNATIONAL CONFERENCE ON RENEWABLE ENERGY RESEARCH AND EDUCATION (RE2-2018)
(2018)
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)