Article
Biochemistry & Molecular Biology
Igor Ryzhov, Alexey Eroshin, Yuriy A. Zhabanov, Daniil N. Finogenov, Pavel A. Stuzhin
Summary: This study investigates the effect of chlorination on the electronic and geometric structures, as well as properties such as chemical bonds and infrared spectra, of metal-free, Al, Ga and In complexes with tetrapyrazinoporphyrazine (TPyzPA) and octachlorotetrapyrazinoporphyrazine (TPyzPACl(8)). Density functional theory (DFT) calculations, NBO-analysis, time-dependent density functional theory (TDDFT) simulations, and analysis of potential energy distribution were carried out to provide insights into these macrocycles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Ceyhun Kucuk, Senay Yurdakul, Belgin Erdem
Summary: The study investigated the properties of 5-iodoindole using theoretical calculations and experimental methods, as well as explored its antimicrobial activity against certain bacteria.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
A. Saral, P. Sudha, S. Muthu, Ahmad Irfan
Summary: The title compound 5-isoquinolinesulfonic acid (5IQSA) is characterized using various spectroscopic techniques, and important parameters such as molecular geometry, vibrational frequencies, and infrared intensities are calculated using Density Functional Theory. The study also investigates the UV-Vis spectra, molecular dynamics, NLO behavior, and topological properties of the compound.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Tevfik Raci Sertbakan, Fatmanur Ozcelik
Summary: This work investigates the properties of 2,6-dibromonaphthalene molecule using quantum chemical calculations. The most stable conformation, vibrational frequencies, and chemical shifts were determined and compared with experimental data. The analysis of charge transfer and electronic energy levels reveals the molecular structure and properties. Additionally, UV/Visible spectroscopy was employed to study the electronic transitions of the molecule.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Spectroscopy
Adriana Kendel, Virna Zavidic, Snezana Miljanic
Summary: The interactions of Hoechst 33258 (H33258) with DNA polynucleotides were studied using surface-enhanced Raman spectroscopy (SERS). The experiments showed that the complexes formed between H33258 and DNA had different stoichiometry ratios. The SERS spectra indicated the aggregation tendency of H33258 and the binding modes of the molecules to DNA. The binding modes included deep insertion into the AT minor groove and partial intercalation between the GC base pairs.
JOURNAL OF RAMAN SPECTROSCOPY
(2022)
Article
Biochemistry & Molecular Biology
Upasana Issar, Richa Arora, Rita Kakkar
Summary: The interaction between minor groove binder Hoechst 33258 and the Dickerson-Drew DNA dodecamer sequence was studied using various computational methods. Twelve different ionization and stereochemical states of the ligand were obtained and docked into B-DNA. Most of these states showed good docking scores and binding energies. Molecular dynamics simulations revealed the best docked state, which had highly negative coulombic interaction energy. However, the polar interactions were offset by unfavorable solvation energies, indicating that nonpolar forces, particularly van der Waals contacts, dominated the interaction.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Inorganic & Nuclear
Sibel Celik, Senay Yurdakul, Belgin Erdem
Summary: The synthesized silver(I) complex showed promising antimicrobial activity against various bacterial species, as evidenced by both experimental data and computational results, indicating its potential as an effective antibacterial agent.
INORGANIC CHEMISTRY COMMUNICATIONS
(2021)
Article
Chemistry, Organic
L. Ravindranath, K. Srishailam, B. Venkatram Reddy
Summary: In this study, Fourier Transform infrared and Raman spectra, NMR spectra, UV-Vis spectra, and quantum chemical calculations were used to analyze three phenol compounds with different functional groups. The experimental data and computational results were in good agreement, providing insights into the electronic transitions, chemical reactivity, and potential applications of these molecules. The presence of intramolecular hydrogen bonds and frontier molecular orbitals were found to play important roles in understanding the properties of the molecules.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Spectroscopy
A. P. Antonyan, M. A. Parsadanyan, N. H. Petrosyan, P. O. Vardevanyan
Summary: Fluorescence spectroscopy was used to investigate the interactions between the bisbenzimidazole compound Hoechst 33258 and bovine serum albumin and calf thymus DNA. The results showed that the binding of the ligand to the proteins and DNA affected the fluorescence intensity, with a decrease in intensity at low protein concentrations and an increase in intensity at high protein concentrations. However, the intensity steadily increased with increasing DNA concentration.
JOURNAL OF APPLIED SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Chad R. Simmons, Alex Buchberger, Skylar J. W. Henry, Alexandra Novacek, Nour Eddine Fahmi, Tara Macculloch, Nicholas Stephanopoulos, Hao Yan
Summary: This study positions a variety of binding molecules in rationally designed and self-assembling DNA crystals and solves their structures via X-ray crystallography, providing insights into the design principles for the spatial arrangement of functional guests within lattices. It opens up new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Dona Benny, Johanan Christian Prasana, Jamal M. Khaled, Ghulam Abbas, S. Muthu
Summary: This research involves experimental, computational, and biological evaluations of a tetrazole derivative. The compound shows potential as an anticonvulsant without causing toxicity.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Multidisciplinary Sciences
Yunusa Umar
Summary: The research computed the molecular structures and electronic data of analgesic drugs carfentanil and acetylfentanyl using quantum chemical code. The results suggest that their piperidine rings have similar geometric parameters, indicating it may be a key structural feature for their analgesic activities. Additionally, introducing a carbomethoxy group into the piperidine ring of these molecules showed minimal effects on their electronic properties.
ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Yuriy A. Zhabanov, Alexey Eroshin, Igor Ryzhov, Ilya A. Kuzmin, Daniil N. Finogenov, Pavel A. Stuzhin
Summary: The Knudsen effusion method with mass spectrometric control was used to study the sublimation enthalpy of metal-free tetrakis(1,2,5-thiadiazolo)porphyrazine and its nickel complex, as well as to determine the geometrical and electronic structure through DFT calculations. The electronic structure of NiTTDPz was further analyzed using the CASSCF method and MCQDPT2. Experimental and theoretical studies were conducted on electronic absorption and vibrational spectra for H(2)TTDPz and NiTTDPz.
Article
Chemistry, Physical
Sibel Celik, Abdullah Atilgan, Meryem Alp, Senay Yurdakul, Zeynep Demircioglu, Namik Ozdemir, Orhan Buyukgungor
Summary: In this work, a new silver (I) complex, [Ag(3-pye)2(H2O)](NO3), has been synthesized and characterized. X-ray diffraction analysis revealed its crystallization in the monoclinic system with the C2/c space group. Computational studies using DFT approach support the experimental results and provide insights into the structural parameters, spectral characteristics, and electronic properties. Hirshfeld surface analysis was also used to identify non-covalent interactions within the crystal structure and visualize its conformity.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Physical
Smita Verma, Rajesh Kumar Patidar, Ratnesh Tiwari, Ravichandiran Velayutham, Nihar Ranjan
Summary: DNA-protein interactions play a crucial role in cellular processes, and understanding the structural basis of nucleic acid recognition is important for developing high-affinity DNA binders. In this study, we designed and synthesized benzimidazole-guanidinium hybrid compounds using a fragment-based strategy and investigated the role of individual fragments in DNA recognition. Our results revealed the interdependent role of the benzimidazole core, polar ends, and DNA composition in imparting sequence-selective binding in the DNA minor groove.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Varun Chahal, Sonam Nirwan, Mallika Pathak, Rita Kakkar
Summary: Pharmacophore and 3D-QSAR models were developed using SLC-0111 derivatives to target human carbonic anhydrase IX (hCA IX), leading to the discovery of effective hCA IX inhibitors. The AADDR.135 model, with high robustness and good predictive ability, identified 1601 compounds in virtual screening. Molecular docking and dynamics simulations unveiled two unique molecules as potential hCA IX inhibitors with higher binding energies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Yan Jiang, Pingping Sun, Lekha Sharma, Baoguang Mao, Rita Kakkar, Tao Meng, Lirong Zheng, Minhua Cao
Summary: The study successfully demonstrated the atomic level identification of catalytic active sites for alkaline HER using MoSe2/CoSe HHSs catalyst model, revealing that it follows the classic bifunctional mechanism. A general two-step Ostwald ripening strategy for mechanism-oriented material design was proposed.
Article
Chemistry, Multidisciplinary
Jogender, Rita Kakkar
Summary: The study showed that graphene and its doped forms can serve as efficient decontaminants, with the introduction of the chemical dopant Fe facilitating chemical adsorption.
STRUCTURAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Shougaijam Premila Devi, Ankit Mittal, Rita Kakkar
Summary: The energetics and mechanisms of different nitrene reactions were deciphered using computational methods B3LYP and MP2. The addition of singlet nitrene to the C-H bond is exothermic, while the addition of triplet nitrene is endothermic and involves the formation of radicals as intermediate products. The Hammond postulate can help distinguish transition state geometries for different reaction steps.
Article
Biochemistry & Molecular Biology
Sonam Nirwan, Varun Chahal, Rita Kakkar
Summary: We investigated the active site of E. coli MurB using the QM/MM methodology and compared the docking results of three series of 4-thiazolidinone derivatives using rigid and flexible docking methods. Flexible docking (IFD) showed improved docking scores and DGbind and confirmed the importance of Tyr254 and Try190 in ligand binding. MD studies further substantiated the findings, with the IFD-LIII j complex being more stable with lower average RMSD and higher average DGbind.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemical Research Methods
Pragati Malik, Rakhi Thareja, Jyoti Singh, Rita Kakkar
Summary: This paper examines the changes in the properties of II-VI Quantum Dots (QDs) when a shell made of the same family material is coated on their surface. It investigates the structural, electronic, and magnetic properties of doped CdS/ZnS core/shell QDs. The results show that the construction of a shell over the bare QDs can greatly affect their optical properties, and the variation of the shell's cation or anion can result in significant changes in the band gap and electrophilicity. Doping the QDs with transition metal ions enhances their properties and introduces magnetism. This paper provides a strategy for developing QDs with desired properties and offers insights into controlling the magnetoelectronic properties of semiconductor materials through doping.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Chemistry, Multidisciplinary
Jyoti Singh, Rakhi Thareja, Pragati Malik, Rita Kakkar
Summary: Density functional theory was used to describe the structural, electronic, and quantum confinement effects observed in II-VI quantum dots. Various properties of the clusters, such as binding energy and band gap, were determined as a function of cluster size. Cadmium clusters were found to have a higher tendency to form clusters with higher coordination numbers, while clusters in mercury sulfide tended to dissociate into parallel layers at certain sizes. Gas molecules were found to adsorb exothermically on CdSe quantum dots, with O-2 and NO2 being the most strongly chemisorbed gases. The study provides insights into the gas sensing properties of the quantum dots being investigated.
JOURNAL OF NANOPARTICLE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Varun Chahal, Rita Kakkar
Summary: This study identifies natural product molecules that can selectively inhibit hCA IX over hCA II using in silico tools. Molecules with the quinoline scaffold showed the highest selectivity, and their stability was confirmed through molecular dynamics simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Himshikha Sharma, Rita Kakkar, Swati Bishnoi, Marilyn Daisy Milton
Summary: A series of A-D-A type push pull molecules based on phenothiazine-5-oxide appended with the p-formylphenyl group were synthesized, and intermolecular D-A interactions in the molecular packing were observed. These fluorescent solids showed on-off-on response to TFA vapors, which was reversed in the presence of TEA vapors. Similar response was also observed in solution, and filter paper strips for TFA sensing were fabricated.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Himshikha Sharma, Shweta Chaudhary, Sonam Nirwan, Rita Kakkar, HuiShan Liew, May-Lee Low, Chun-Wai Mai, Ling-Wei Hii, Chee-Onn Leong, Marilyn Daisy Milton
Summary: A series of dicationic N, N'-disubstituted benzimidazolium salts with Br- and PF6- as the counter anions were synthesized, showing selective turn-off fluorescence response toward Fe3+ ions in aqueous solution and synergism with doxorubicin in combinatorial treatment of breast cancer cells. Molecular docking studies revealed the binding affinity of one of the salts with checkpoint kinase 2 protein.
Review
Plant Sciences
Dwaipayan Sinha, Soumi Datta, Reema Mishra, Preeti Agarwal, Tripti Kumari, Sherif Babatunde Adeyemi, Arun Kumar Maurya, Sharmistha Ganguly, Usman Atique, Sanchita Seal, Laxmi Kumari Gupta, Shahana Chowdhury, Jen-Tsung Chen
Summary: Arsenic, a metalloid, is mainly found in soil and water. Excessive levels of arsenic are toxic to living organisms, making it a global concern. Humans can absorb arsenic through polluted water and contaminated food, while plants are more susceptible to arsenic poisoning due to their inability to move and their reliance on roots for nutrients. Arsenic competes with phosphorus and disrupts physiological processes in plants, leading to decreased yield and biomass. Various mitigation strategies, including agronomic practices and genetic manipulation, can help reduce arsenic absorption by plants and address the negative effects.
Article
Multidisciplinary Sciences
Tripti Kumari, Muskan Gill, Divya Saini, Monika Keisham
Summary: Heavy metals in soil and water pose a serious threat to all life forms due to their bio-accumulative nature. Sawdust from mango tree wood has been tested as a low-cost and efficient adsorbent for the quantitative removal of heavy metal ions from aqueous solutions. The results indicate that plants grown on soil mixed with sawdust have significantly lower heavy metal content, proving sawdust to be a sustainable solution for reducing heavy metal pollution in soil and water.
PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY
(2023)
Article
Chemistry, Applied
Preeti Yadav, Badri Parshad, Krishna, Antara Sharma, Rita Kakkar, Sunil K. Sharma
Summary: A C3-symmetric triazole-based multivalent dendritic architecture was used to investigate its metal binding ability towards various metal ions. The architecture showed a high affinity for Cu(II) ions, forming a solid complex with a blue shift in the dd-band of Cu(II) chloride. X-band EPR spectra confirmed a distorted tetrahedral geometry for the complex. DFT calculations revealed a high exothermicity in the complexation reactions with Cu(II), indicating a strong affinity between Cu(II) and the dendritic structure.
INDIAN JOURNAL OF CHEMICAL TECHNOLOGY
(2023)
Article
Chemistry, Physical
Mudita Nagpal, Rita Kakkar
Summary: In this study, hierarchically porous Ca-Mg mixed oxide (Hr-CaO.MgO) was synthesized using the co-precipitation method. The as-synthesized Hr-CaO.MgO exhibited a dumbbell morphology and possessed hierarchical porosity with a surface area of 44.5 m(2) g(-1). The adsorption efficiency of Hr-CaO.MgO was investigated using four dyes, demonstrating highly selective adsorption of Congo red (CR) individually and in binary dye mixtures. Batch adsorption studies revealed that CR adsorption on Hr-CaO.MgO followed the Langmuir isotherm model and pseudo second order kinetic model. The selective adsorption of CR on Hr-CaO.MgO was attributed to electrostatic attraction and hydrogen bonding. Therefore, Hr-CaO.MgO is a potential candidate for selective adsorption of CR from wastewaters.
APPLIED SURFACE SCIENCE ADVANCES
(2022)
Review
Chemistry, Multidisciplinary
Ankit Mittal, Rita Kakkar
Summary: The medicinal herb liquorice, derived from the root and rhizomes of Glycyrrhiza species, has been widely used for the treatment of various diseases. Compounds isolated from liquorice root, including retrochalcones, have diverse pharmacological applications such as antioxidant, anti-inflammatory, anti-cancer, anti-bacterial, anti-diabetic, anti-obesity, and anti-parasitic effects.
RESULTS IN CHEMISTRY
(2021)
Article
Chemistry, Physical
A. Aathif Basha, Attar Kubaib, Mohammad Azam
Summary: The properties of a set of compounds were comprehensively assessed using various analytical techniques, revealing their stability and favorable drug-like characteristics. Potential antiviral and antioxidant properties were predicted, indicating promise for biological efficacy.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Meiqi Liu, Baoming Hou, Yuheng Li, Yuyu Pan, Bing Yang
Summary: This paper investigates the application potential of thermally activated delayed fluorescent (TADF) molecules with donor-acceptor-donor-acceptor pi-conjugated macrocycle structures in organic light-emitting diodes. The study finds that the macrocyclic structure has a smaller energy gap between the first singlet excited state and the first triplet excited state compared to the linear structure. The TADF efficiency is also analyzed and explained based on spin-orbit coupling and intersystem crossing rates.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Run Liu, Jiahui Liu, Jiarui Fang, Xiruo Bai, Dan Wang, Yixuan Qie, Shuqi Zu, Guancheng Wang, Xinyi Sui, Runyao Chang, Yizhu Wang, Ziheng Li
Summary: This paper investigates the remodeling effect of H2O molecules and their adsorption behavior on Co2+-doped SnO2 (221) crystal plane materials. The results show that H2O molecules remodel the crystal plane by creating oxygen defects, leading to hydroxylation. The hydroxylated crystal surface adsorbs O2 and then H2O molecules, affecting the electrical conductivity of the crystal plane.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Marisol Ibarra-Rodriguez, Paul Horley, Mario Sanchez
Summary: In this study, the functionalized borophene was investigated as a potential sensor or transporter of glucose for biomedical applications. The adsorption of glucose molecules on different boron-based complexes was studied, and the results showed that these complexes have high binding energies and can efficiently adsorb glucose molecules. The findings suggest that borophene-based systems with different oxidation states hold promise for intelligent drug delivery and biosensor design.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Syed Hassan Sarwar, Saad Jawaid Khan, Syed Faraz Jawed
Summary: The medical community is currently focusing on targeted and controlled drug delivery, and many researchers are utilizing computational resources to understand drugnanocarrier combinations and develop targeted drug delivery systems. This study used molecular dynamics to investigate the encapsulation capacity of Carbazochrome, a hemostatic drug, in Single-Walled Carbon Nanotubes of different morphological variations. The results showed that the nanotube radius and length had the most significant impact on the encapsulation capacity, followed by nanotube chirality. Temperature also affected the drug encapsulation when the nanotube radius was not very large and the chiral angle was near 30 degrees.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Yinquan Sui, Mengying Sun, Yongxin Wang, Zhitong Xu, Jinglu Yan, Huanpeng Liu
Summary: In this study, the structural and hydrogen storage properties of loaded Pt atoms were investigated using density functional theory (DFT) with and without substitution of B atoms on the edges of conical graphene layers (CGL). It was found that the position of the substituted B atom at the edge of the CGL has an important effect on the position of the loaded Pt atom and its hydrogen adsorption and storage properties.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
