1
|
Jurkowski M, Kogut M, Sappati S, Czub J. Why Are Left-Handed G-Quadruplexes Scarce? J Phys Chem Lett 2024; 15:3142-3148. [PMID: 38477716 PMCID: PMC10961827 DOI: 10.1021/acs.jpclett.3c03589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods. Our results reveal that right-handed G4s exhibit greater thermodynamic and kinetic stability as a result of favorable sugar-phosphate backbone conformations in guanine tracts. Moreover, while hydrogen-bonding patterns influence helicity-specific G4 loop conformations, they minimally affect stability differences. We also elucidate the strong correlation between helicity and the strand progression direction, essential for G4 structures. These findings deepen our understanding of G4s, providing molecular-level insights into their structural and energetic preferences, which could inform the design of novel nanodevices.
Collapse
Affiliation(s)
- Michał Jurkowski
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Mateusz Kogut
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Subrahmanyam Sappati
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| |
Collapse
|
2
|
Słabońska J, Sappati S, Marciniak A, Czub J. Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline. ACS Med Chem Lett 2024; 15:265-269. [PMID: 38352844 PMCID: PMC10860170 DOI: 10.1021/acsmedchemlett.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
The role of short strong hydrogen bonds (SSHBs) in ligand-target binding remains largely unexplored, thereby hindering a potentially important avenue in rational drug design. Here we investigate the interaction between the antituberculosis drug bedaquiline (Bq) and the mycobacterial ATP synthase to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity. Our ab initio molecular dynamics simulations reveal that this bond belongs to the SSHB category and accounts for a substantial fraction of the target binding free energy. We also demonstrate that the presence of an extra acidic residue, i.e., aspartic acid at position 32 (D32), found exclusively in mycobacteria, cooperatively enhances the HB strength, ensuring specificity for the mycobacterial target. Consistently, we show that the removal of D32 markedly weakens the affinity, leading to Bq resistance associated with mutations of D32 to nonacidic residues. By designing simple Bq analogs, we then explore the possibility to overcome the resistance and potentially broaden the Bq antimicrobial spectrum by making the SSHB independent of the presence of the extra acidic residue.
Collapse
Affiliation(s)
- Joanna Słabońska
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
| | - Subrahmanyam Sappati
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
| | - Antoni Marciniak
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
- Department
of Applied Physics, KTH Royal Institute
of Technology, SE-171 65 Solna, Sweden
| | - Jacek Czub
- Department
of Physical Chemistry, Gdańsk University
of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
- BioTechMed
Center, Gdańsk University of Technology, Narutowicza St 11/12, Gdańsk 80-233, Poland
| |
Collapse
|
3
|
Saha T, Sappati S, Das S. An insight into the mixed quantum mechanical-molecular dynamic simulation of a Zn II-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations. Int J Biol Macromol 2023:125305. [PMID: 37315676 DOI: 10.1016/j.ijbiomac.2023.125305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
An important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule of water bound to ZnII. It arrests degradation of HCur to a considerable extent that was realized by taking it in phosphate buffer and in biological milieu. The structure was obtained by DFT calculations. Stable adduct formation was identified between optimized structures of HCur and [Zn(Cur)] with DNA (PDB ID: 1BNA) through experiments validated with multiscale modeling approach. Molecular docking studies provide 2D and 3D representations of binding of HCur and [Zn(Cur)] through different non-covalent interactions with the nucleotides of the chosen DNA. Through molecular dynamics simulation, a detailed understanding of binding pattern and key structural characteristics of the generated DNA-complex was obtained following analysis by RMSD, RMSF, radius of gyration, SASA and aspects like formation of hydrogen bonds. Experimental studies provide binding constants for [Zn(Cur)] with calf thymus DNA at 25 °C that effectively helps one to realize its high affinity towards DNA. In the absence of an experimental binding study of HCur with DNA, owing to its tendency to degrade in solution, a theoretical analysis of the binding of HCur to DNA is extremely helpful. Besides, both experimental and simulated binding of [Zn(Cur)] to DNA may be considered as a case of pseudo-binding of HCur to DNA. In a way, such studies on interaction with DNA helps one to identify HCur's affinity for cellular target DNA, not realized through experiments. The entire investigation is an understanding of experimental and theoretical approaches that has been compared continuously, being particularly useful when a molecule's interaction with a biological target cannot realized experimentally.
Collapse
Affiliation(s)
- Tanmoy Saha
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India
| | - Subrahmanyam Sappati
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland; Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland
| | - Saurabh Das
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India.
| |
Collapse
|
4
|
Shilkar OA, Adhikari R, Sappati S, Godi S, Desai AM. A first-principles study of electronic and magnetic properties of 4d transition metals doped in Wurtzite GaN for spintronics applications. J Mol Model 2023; 29:200. [PMID: 37269432 DOI: 10.1007/s00894-023-05529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/23/2023] [Indexed: 06/05/2023]
Abstract
We studied the electronic and magnetic properties of wurtzite GaN (w-GaN) doped with different concentrations of the 4d transition metal ions Nb, Mo, and Ru. We incorporated spin-polarized plane-wave density functional theory within an ultrasoft pseudopotential formalism. The 4d transition metals were doped at different geometrical sites to determine the geometry with the lowest total energy and the one that induced the largest magnetization. A spin-spin interaction study was performed to determine whether the doped compound was ferromagnetic or antiferromagnetic. The origin of magnetization in the transition metal-doped w-GaN compounds is due to the p-d hybridization of the nitrogen and 4d transition metals. From the bulk modulus results, we inferred that the structural integrity is preserved under compressive loads after doping w-GaN with these 4d transition metal ions. Our results indicate that these compounds can be used in spintronic applications.
Collapse
Affiliation(s)
- Omkar A Shilkar
- Department of Physics, Parvatibai Chowgule College of Arts and Science, Margao, 403602, Goa, India
- School of Physical and Applied Sciences, Goa University, Taleigão, 403206, Goa, India
| | - Rajendra Adhikari
- Department of Physics, Kathmandu University, Dhulikhel, 45200, Nepal
| | - Subrahmanyam Sappati
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, 80-233, Poland
- BioTechMed Center, Gdańsk University of Technology, Gdańsk, 80-233, Poland
| | - Shreya Godi
- Department of Physics, Parvatibai Chowgule College of Arts and Science, Margao, 403602, Goa, India
- School of Physical and Applied Sciences, Goa University, Taleigão, 403206, Goa, India
| | - Ashish M Desai
- Department of Physics, Parvatibai Chowgule College of Arts and Science, Margao, 403602, Goa, India.
| |
Collapse
|
5
|
Hering A, Stefanowicz-Hajduk J, Dziomba S, Halasa R, Krzemieniecki R, Sappati S, Baginski M, Ochocka JR. Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies. Antioxidants (Basel) 2023; 12:antiox12051016. [PMID: 37237882 DOI: 10.3390/antiox12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Mangiferin is a strong antioxidant that presents a wide range of biological activities. The aim of this study was to evaluate, for the first time, the influence of mangiferin on tyrosinase, an enzyme responsible for melanin synthesis and the unwanted browning process of food. The research included both the kinetics and molecular interactions between tyrosinase and mangiferin. The research proved that mangiferin inhibits tyrosinase activity in a dose-dependent manner with IC50 290 +/- 6.04 µM, which was found comparable with the standard kojic acid (IC50 217.45 +/- 2.54 µM). The mechanism of inhibition was described as mixed inhibition. The interaction between tyrosinase enzyme and mangiferin was confirmed with capillary electrophoresis (CE). The analysis indicated the formation of two main, and four less significant complexes. These results have also been supported by the molecular docking studies. It was indicated that mangiferin binds to tyrosinase, similarly to L-DOPA molecule, both in the active center and peripheral site. As it was presented in molecular docking studies, mangiferin and L-DOPA molecules can interact in a similar way with surrounding amino acid residues of tyrosinase. Additionally, hydroxyl groups of mangiferin may interact with amino acids on the tyrosinase external surface causing non-specific interaction.
Collapse
Affiliation(s)
- Anna Hering
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, 80-210 Gdansk, Poland
| | | | - Szymon Dziomba
- Department of Toxicology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Rafal Halasa
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Radoslaw Krzemieniecki
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Subrahmanyam Sappati
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland
| | - Jadwiga Renata Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, 80-210 Gdansk, Poland
| |
Collapse
|
6
|
Ezzemani W, Kettani A, Sappati S, Kondaka K, El Ossmani H, Tsukiyama-Kohara K, Altawalah H, Saile R, Kohara M, Benjelloun S, Ezzikouri S. Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants. J Biomol Struct Dyn 2022:1-22. [PMID: 35549819 DOI: 10.1080/07391102.2022.2075468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel epitopes were identified as immunogenic triggering immune responses and no toxic after investigation with in silico tools. Furthermore, we found these peptide vaccine candidates showed a significant binding affinity for MHC I and MHC II alleles in molecular docking investigations. We consider them to be promising targets for developing peptide-based vaccines against SARS-CoV-2. Subsequently, we designed two efficient multi-epitopes vaccines against the SARS-CoV-2, the first one based on potent MHC class I and class II T-cell epitopes of S (FPNITNLCPF-NYNYLYRLFR-MFVFLVLLPLVSSQC), M (MWLSYFIASF-GLMWLSYFIASFRLF), E (LTALRLCAY-LLFLAFVVFLLVTLA), and N (SPRWYFYYL-AQFAPSASAFFGMSR). The second candidate is the result of the tailoring of the first designed vaccine according to three classes of SARS-CoV-2 variants. Molecular docking showed that the protein-protein binding interactions between the vaccines construct and TLR2-TLR4 immune receptors are stable complexes. These findings confirmed that the final multi-epitope vaccine could be easily adapted to new viral variants. Our study offers a shortlist of promising epitopes that can accelerate the development of an effective and safe vaccine against the virus and its adaptation to new variants.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Subrahmanyam Sappati
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland.,BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Kavya Kondaka
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, AMSSNuR, Rabat, Morocco
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.,Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| |
Collapse
|
7
|
Sujith M, Vishnu EK, Sappati S, Oliyantakath Hassan MS, Vijayan V, Thomas KG. Ligand-Induced Ground- and Excited-State Chirality in Silicon Nanoparticles: Surface Interactions Matter. J Am Chem Soc 2022; 144:5074-5086. [PMID: 35258297 DOI: 10.1021/jacs.1c13698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Silicon-based light-emitting materials have emerged as a favorable substitute to various organic and inorganic systems due to silicon's high natural abundance, low toxicity, and excellent biocompatibility. However, efforts on the design of free-standing silicon nanoparticles with chiral non-racemic absorption and emission attributes are rather scare. Herein, we unravel the structural requirements for ligand-induced chirality in silicon-based nanomaterials by functionalizing with D- and L-isomers of a bifunctional ligand, namely, tryptophan. The structural aspects of these systems are established using high-resolution high-angle annular dark-field imaging in the scanning transmission electron microscopy mode, solid-state nuclear magnetic resonance, Fourier transform infrared, and X-ray photoelectron spectroscopy. Silicon nanoparticles capped with L- and D-isomers of tryptophan displayed positive and negative monosignated circular dichroic signals and circularly polarized luminescence indicating their ground- and excited-state chirality. Various studies supported by density functional theory calculations signify that the functionalization of indole ring nitrogen on the silicon surface plays a decisive role in modifying the chiroptical characteristics by generating emissive charge-transfer states. The chiroptical responses originate from the multipoint interactions of tryptophan with the nanoparticle surface through the indole nitrogen and -CO2- groups that can transmit an enantiomeric structural imprint on the silicon surface. However, chiroptical properties are not observed in phenylalanine- and alanine-capped silicon nanoparticles, which are devoid of Si-N bonds and chiral footprints. Thus, the ground- and excited-state chiroptics in tryptophan-capped silicon nanoparticles originates from the collective effect of ligand-bound emissive charge-transfer states and chiral footprints. Being the first report on the circularly polarized luminescence in silicon nanoparticles, this work will open newer possibilities in the field of chirality.
Collapse
Affiliation(s)
- Meleppatt Sujith
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - E Krishnan Vishnu
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Subrahmanyam Sappati
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Muhammed Shafeek Oliyantakath Hassan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - K George Thomas
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| |
Collapse
|
8
|
Nedyalkova M, Vasighi M, Sappati S, Kumar A, Madurga S, Simeonov V. Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach. Pharmaceuticals (Basel) 2021; 14:ph14121328. [PMID: 34959727 PMCID: PMC8704597 DOI: 10.3390/ph14121328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
The lack of medication to treat COVID-19 is still an obstacle that needs to be addressed by all possible scientific approaches. It is essential to design newer drugs with varied approaches. A receptor-binding domain (RBD) is a key part of SARS-CoV-2 virus, located on its surface, that allows it to dock to ACE2 receptors present on human cells, which is followed by admission of virus into cells, and thus infection is triggered. Specific receptor-binding domains on the spike protein play a pivotal role in binding to the receptor. In this regard, the in silico method plays an important role, as it is more rapid and cost effective than the trial and error methods using experimental studies. A combination of virtual screening, molecular docking, molecular simulations and machine learning techniques are applied on a library of natural compounds to identify ligands that show significant binding affinity at the hydrophobic pocket of the RBD. A list of ligands with high binding affinity was obtained using molecular docking and molecular dynamics (MD) simulations for protein–ligand complexes. Machine learning (ML) classification schemes have been applied to obtain features of ligands and important descriptors, which help in identification of better binding ligands. A plethora of descriptors were used for training the self-organizing map algorithm. The model brings out descriptors important for protein–ligand interactions.
Collapse
Affiliation(s)
- Miroslava Nedyalkova
- Inorganic Chemistry Department, Faculty of Chemistry and Pharmacy “St Kliment Ohridski”, University of Sofia, 1164 Sofia, Bulgaria
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
- Correspondence:
| | - Mahdi Vasighi
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran;
| | | | - Anmol Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA;
| | - Sergio Madurga
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08007 Barcelona, Spain;
| | - Vasil Simeonov
- Analytical Chemistry Department, Faculty of Chemistry and Pharmacy “St Kliment Ohridski”, University of Sofia, 1164 Sofia, Bulgaria;
| |
Collapse
|
9
|
Chatterjee A, Chatterjee J, Sappati S, Sheikh T, Umesh RM, Ambhore MD, Lahiri M, Hazra P. Emergence of Aggregation Induced Emission (AIE), Room-Temperature Phosphorescence (RTP), and Multistimuli Response from a Single Organic Luminogen by Directed Structural Modification. J Phys Chem B 2021; 125:12832-12846. [PMID: 34762798 DOI: 10.1021/acs.jpcb.1c08126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multifunctional organic luminogens exhibiting simultaneous aggregation induced emission (AIE), room-temperature phosphorescence (RTP), and mechanochromism have recently attracted considerable attention owing to their potential applications in optoelectronics and bioimaging. However, a comprehensive correlation among these three distinguished properties is yet to be unveiled, which will help to decipher defined methodologies to design future generation multifunctional organic materials. Herein, we have demonstrated a route to obtain a multifunctional organic luminogen, starting from an ACQphore (TPANDI) by simple structural engineering. We have shown that a slight reduction in length of the planar acceptor moieties can effectively inhibit the undesirable π-π stacking interaction between molecules in the condensed state and thereby cause an ACQ to AIE type transformation from TPANDI to TPANMI and TPAPMI. Both TPANMI and TPAPMI exhibit RTP properties (even in ambient condition) because of the presence of a reasonably low singlet-triplet energy gap (ΔEST). In our study, these two luminogens were found to be mechano-inactive. Interestingly, an insertion of cyano-ethylene group and benzene linker in between the triphenylamine and phthalimide moieties introduced another luminogen TPACNPMI, which can simultaneously exhibit AIE, RTP, and mechanochromic properties.
Collapse
Affiliation(s)
- Abhijit Chatterjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Joy Chatterjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Subrahmanyam Sappati
- Soft Condensed Matter, Raman Research Institute, C. V. Raman Avenue, Sadashivanagar, Bengaluru, Karnataka India 560080
| | - Tariq Sheikh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Rintu M Umesh
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Madan D Ambhore
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Mayurika Lahiri
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008.,Centre for Energy Science, Indian Institute of Science Education and Research (IISER), Pune. Dr. Homi Bhabha Road, Pashan, Pune, India 411008
| |
Collapse
|
10
|
Das K, Sappati S, Bisht GS, Hazra P. Proton-Coupled Electron Transfer in the Aqueous Nanochannels of Lyotropic Liquid Crystals: Interplay of H-Bonding and Polarity Effects. J Phys Chem Lett 2021; 12:2651-2659. [PMID: 33689368 DOI: 10.1021/acs.jpclett.1c00207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A molecular-level description of the aqueous nanochannels in lyotropic liquid crystals (LLCs) is crucial for their widespread utilization in diverse fields. Herein, the polarity and hydrogen bonding effects of LLC water molecules have been simultaneously explored using a single probe, 4'-N,N-dimethylamino-3-hydroxyflavone (DMA3HF), by the unique multiparametric sensitivity of the excited state proton-coupled electron transfer (PCET) phenomenon. The decreased ESIPT efficiency and the significantly retarded ESIPT dynamics (>20 times) of DMA3HF in the LLC phases suggests the dominant influence of strong hydrogen-bonded solute-solvent complexes that leads to a high activation barrier for ESIPT in the mesophases. The effects of hydrogen bonding on ESIPT have been elucidated by enhanced sampling techniques based on classical MD simulations of DMA3HF in explicit water. ESIPT via an extended hydrogen-bonded water wire is associated with a significantly high ESIPT activation barrier, substantiating the experimentally observed slow ESIPT dynamics inside the LLCs.
Collapse
Affiliation(s)
- Konoya Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | | | - Girish Singh Bisht
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|
11
|
Das K, Sappati S, Hazra P. Peculiar hydrogen bonding behaviour of water molecules inside the aqueous nanochannels of lyotropic liquid crystals. Phys Chem Chem Phys 2020; 22:6210-6221. [DOI: 10.1039/c9cp06405b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The hydrogen bonding abilities of the LLC water molecules and their effects on intramolecular hydrogen bonds of the target probe molecules.
Collapse
Affiliation(s)
- Konoya Das
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Subrahmanyam Sappati
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Partha Hazra
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
- Centre for Energy Science
| |
Collapse
|
12
|
Sappati S, George L, Swamy VP, Devi RN, Ghosh P. Descriptors to Predict Dye‐Sensitized Semiconductor Based Photocatalyst for Hydrogen Evolution Reaction. ChemCatChem 2019. [DOI: 10.1002/cctc.201901924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Subrahmanyam Sappati
- Chemistry DepartmentIndian Institute of Science Education and Research Pune 411008 India
| | - Leena George
- Catalysis DivisionNational Chemical Laboratory Pune 411008 India
| | - Vincent Paul Swamy
- Organic Chemistry DivisionNational Chemical Laboratory Pune 411008 India
| | - R. Nandini Devi
- Catalysis DivisionNational Chemical Laboratory Pune 411008 India
| | - Prasenjit Ghosh
- Physics Department and Centre for Energy SciencesIndian Institute of Science Education and Research Pune 411008 India
| |
Collapse
|
13
|
Satpathi S, Sappati S, Das K, Hazra P. Structural characteristics requisite for the ligand-based selective detection of i-motif DNA. Org Biomol Chem 2019; 17:5392-5399. [DOI: 10.1039/c9ob01020c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new approach has been explored to detect i-motif DNA structures over its complementary GQ DNA based on the hemi-protonated cytosine–cytosine (C+–C) base pairing recognition. This approach also shows its versatility by detecting various i-motif DNA structures with different chain lengths, molecularity and sizes, etc.
Collapse
Affiliation(s)
- Sagar Satpathi
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Subrahmanyam Sappati
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Konoya Das
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
| | - Partha Hazra
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune
- India
- Centre for Energy Science
| |
Collapse
|
14
|
George L, Sappati S, Ghosh P, Devi RN. Sensitizing with short conjugated molecules: Multimodal anchoring on ZnO nanoparticles for enhanced electron transfer characteristics, stability and H 2 evolution. Catal Today 2018. [DOI: 10.1016/j.cattod.2017.09.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
Abstract
Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak.
Collapse
Affiliation(s)
- Subrahmanyam Sappati
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ralph Gebauer
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Prasenjit Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| |
Collapse
|
16
|
Koninti RK, Sappati S, Satpathi S, Gavvala K, Hazra P. Spectroscopy and Dynamics of Cryptolepine in the Nanocavity of Cucurbit[7]uril and DNA. Chemphyschem 2016; 17:506-15. [PMID: 26650669 DOI: 10.1002/cphc.201501011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 12/07/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Raj Kumar Koninti
- Department of Chemistry; Indian Institute of Science Education and Research (IISER); Pune 411008 Maharashtra India
| | - Subrahmanyam Sappati
- Department of Chemistry; Indian Institute of Science Education and Research (IISER); Pune 411008 Maharashtra India
| | - Sagar Satpathi
- Department of Chemistry; Indian Institute of Science Education and Research (IISER); Pune 411008 Maharashtra India
| | - Krishna Gavvala
- Department of Chemistry; Indian Institute of Science Education and Research (IISER); Pune 411008 Maharashtra India
| | - Partha Hazra
- Department of Chemistry; Indian Institute of Science Education and Research (IISER); Pune 411008 Maharashtra India
| |
Collapse
|
17
|
Dhara B, Sappati S, Singh SK, Kurungot S, Ghosh P, Ballav N. Coordination polymers of Fe(iii) and Al(iii) ions with TCA ligand: distinctive fluorescence, CO2uptake, redox-activity and oxygen evolution reaction. Dalton Trans 2016; 45:6901-8. [DOI: 10.1039/c6dt00009f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Remarkable differences in the physicochemical properties of metal–organic gels of Fe(iii) and Al(iii) ions with the TCA ligand is reported.
Collapse
Affiliation(s)
| | | | | | | | - Prasenjit Ghosh
- Department of Chemistry
- IISER Pune
- India
- Department of Physics
- IISER Pune
| | | |
Collapse
|